factorio 1.1.6
miniloader 1.13.0
I have not narrowed this to a copy/paste, blueprint or manual placement, but sometimes miniloaders will only move materials on one lane.
My workaround: delete and replace (manually or by bot)

Sounds like a bad interaction with another mod, possibly.

I can try later with only miniloaders mod!
Thanks.

FYI
Early-Armor-Grid 0.0.3
ElectricTrain 1.1.2
FasterStart 1.1.1
miniloader 1.13.0
some-disableenemygeneration 1.1.0
some-spidertron 1.1.0
SpidertronWaypoints 1.7.2
TinyStart 1.1.0
train-pubsub 1.1.4
VehicleSnap 1.18.4

I can duplicate in new sandbox map with only 'base' and 'miniloader.'

Pasting a miniloader over a miniloader stops one lane working - this is flow-direction dependent.

If the flow is south to north, the right lane stops.
If the flow is north to south the left lane stops.

If the flow is east to west, the upper lane stops.
If the flow is west to east the lower lane stops.

Can you go step by step so I can reproduce locally?

Sure. I just went through these steps in 1.1.6
New sandbox map - with only 'base' 1.1.6 and 'miniloader' 1.13.0. mod enabled - to ensure no other mod interactions.

Acknowledge opening dialog <TAB>
Accept all 'sandbox' prompts. This should give you some materials to work with: belts and plates.

Disable 'snap miniloaders' in Mod Settings.
Craft two miniloaders - tier probably does not matter, but I used the base miniloaders and transport belts.

Make a belt loop. Replace two belt sections with back to back miniloaders - in the same flow as the belt loop.
Fill the belt with the iron plates. Fill the inner lane manually, the miniloader pair will swap lanes so that eventually both lanes will be full..
Copy the outgoing miniloader -- without deleting the outgoing miniloader, paste the 'copy' onto the outgoing miniloader.
One lane will stop working.

hth

This is the BP string of my test setup, described above:

0eNqd1eFugyAQAOB3ud+0AaqivsqyGKuXhVTRAF3WNb77sCZNN+3C9Z8IfngHB1c4dmccrTYeyivoZjAOyrcrOP1h6m5+5y8jQgnaYw8MTN3PLW9r48bB+t0ROw8TA21a/IJSTO8M0HjtNS7SrXGpzLk/og0DnhkMxsGFzwYzzxqondynDC7hQezTMEOrLTZLv5zYCpYvwDzAG9QhnuKkf0ziYUGC0zvca6O7oW7R7rRxaH3oXun/4AyGT7RWt1g5XzenyulvvC1ba4ex+gPxvSgKKXJ1T6icwVE3p/NqcOjNOVe5kMtovpX7jBbJ8/xntEgEMRLJD//GoaKX+kBa6TzapZVPEe0mj9Xzy002XMHpsIiCXzhJntS7kPS6XAWfbcEvnCRxcPxJQnPTaJeWiIy8beNcepnFuTl512644Sq8XZvlwy3LIBxKbinDXCSqkEpyJYSS0/QDL911TQ==

[Edit: there is some other odd interaction that I may describe later.]

The 'other odd interaction'

using the BP string below, if I fill the chest, the miniloader pair in the belt loop does not swap lanes as they would if I fill the belt manually using the 'Z' key.
You might want a character and personal roboport for this one. We will be tearing down and rebuilding this BP.
In console, paste /c game.player.create_character()
Craft MK2 power armor. Craft and place into armor grid: personal batteries, personal roboport and a portable fusion reactor.
Craft several construction bots.
Below, where you see the instructions 'Delete and rebuild loop.' let the bots do the heavy-lifting! :)

Steps:
Place BP - let bots build.
Do not put anything in the chest, yet.
Manually put a few plates on the inner lane of the loop - not a lot, just enough to observe the miniloader pair swapping lanes.
Delete and rebuild loop. Place some plates on the outer lane. No lane swapping. (Maybe just an artifact of the packaged inserters!)

Delete and rebuild loop. Place one plate on the inner stub belt coming from the chest. No lane swap at miniloader pair.
Let the plate make a full circuit around the belt loop. After the single plate exits the miniloader pair, add more plates to the inner stub belt. No lane swapping at miniloader pair - even after the plates make several circuits around the belt loop.

Delete and rebuild loop. Place two plates on the stub belt coming from the chest. No lane swap at miniloader pair.
Let the plates make a full circuit around the belt loop. Now, we have lane swapping at the miniloader pair.
[EDIT: this is not 100% repeatable]

Delete and rebuild loop. Place all of one plate-type into the chest. No lane swap at miniloader pair.
[EDIT: this is not 100% repeatable]

Delete and rebuild loop. Place two plates onto belt stub coming from the chest.
Before the plates make a full circuit around the belt loop, place the remaining plates of same plate-type into chest.
No lane swap at miniloader pair.

Delete and rebuild loop. Place two plates onto belt stub coming from the chest.
Let the plates make a full circuit around the belt loop. Now, we have lane swapping at the miniloader pair.
Place the remaining plates of same plate-type into chest. Lane swap at miniloader pair.

[EDIT I have another odd interaction.]
Delete and rebuild loop. Place one plate on the inner lane of the belt loop just before the incoming miniloader.
Immediately after this plate goes into the incoming miniloader, place another plate on the belt.
The first plate will swap lanes, the second plate will not swap lanes.
After the plates make a complete circuit of the belt loop, the second plate will swap lanes at the miniloader pair.
Both plates will be on the inner lane of the belt loop.

(I will follow these instruction after posting, for verification. If I find an error, I will edit with the '[EDIT]' indicator.) <- Finished.

0eNqVlttugzAMht/F11Al4RDgVaYJUbC2aDSgJJ3WVbz7QqtV3TgovgwOXxL/9i9f4difcTRKO6iuoNpBW6hermDVm276+Zu7jAgVKIcniEA3p3nlTKPtOBgXH7F3MEWgdIdfUPHpNQLUTjmFd9Jtcan1+XRE4zdsMSIYB+t/G/R8qkfF4pBFcIGKHTJ/QKcMtvewmKIFV9C53HNXSEk4iT+R/twwX+GmD+5JadUPTYcmVtqicT68hLNNeATDJxqjOqyta9qP2qpvvKW2M8NYL0G8LAUv5G86xQwcVftxXmxmB1nmj51r6cnC08MoAub0tAdx5YNrHWIft+9oV6BsvygKmnjbN6Rp90+6eFc7Hy0YkwUXO/KVtIdsSkgsQk58iGDJ7jM4Cy6XhFItPNyfSPbEw/0p3er7dI2bkLksiJvS/VSstw7P6J0tQgyV53QrCgPLYDCNWwRzaYkoyUUbxBX0JgvjcnLRrnD9oHEbSqqnGSYC70n23oUFT2UppGCScymm6QfW++di

Thanks! I was able to resolve the problem when pasting a blueprint over an existing miniloader.
The swapping of items between lanes when passing through a miniloader is entirely dependent on the details of inserter timing, so there is no guarantee of consistency there.

Thank you.

Fix confirmed.
Thank you

therax, this is still an issue. https://imgur.com/S0MUopY
1.1.8 base/1.13.1 miniloader and the same modlist from OP. (except SpidertronWaypoints updated to 1.7.3)
I cannot readily duplicate it, but I have a strong suspicion that it is still related to pasting BPs over miniloader ghosts -or- existing miniloaders.
-I have a rather large yellow science build that took several pastes to get laid out -- fog of war issues.
At this time, I am not requesting any bother on your end as I try to narrow down a repeatable method to duplicate it.
Thank you!

I can confirm this is an issue (atleast in 1.1.12) and it does manifests only when i plop a BP with miniloaders over existing miniloaders, in my case. As i use your mod extensively, the only workaround i found for myself is either only build BP once, or if for some reason i need to plop it over existing loaders - i just make a copy of bp and remove miniloders from it. This saves the hassle of fixing each loader's laning problem manually later.

@ Fywaprold,
Thank you for the confirmation.
I have found that after I notice this issue, I can copy/paste the BP back on top of the errant miniloader(s) and it/they work.

If either of you find a reproducible way to get this to happen, I'm still interested in finding and squashing this bug. :)

Sorry, therax, I have been playing Valheim lately.
When I get back to Factorio, I will try to reproduce.

I am encountering this issue occasionally, though I have not devised a reliable way to reproduce it. Simply toggling the direction of the miniloader is enough to resolve it.

Factorio 1.1.53
Miniloader 1.14.6

I've been seeing the one lane behavior periodically in my game, so I disabled every mod except Miniloader and used the game scenario Rocket rush to have the items to test.

It always manifests itself in my train stations, so I suspect it has something to do with bots building blueprints that have Snap to grid enabled, with the Grid position "Relative". Here's my test blueprint string.

Replacing the string with a link since it was so long.

https://factorioprints.com/view/-MybzBoozAg-0ID0cNnD

If I left click and drag to build 3 or 4 of those, there's a chance 1 or more will only use one side of the belt. Sometimes they all work, but if I pick them back up and repeat, I can usually see the bug within 2 or 3 attempts.