I first noticed this issue in Bobs mod run, but was able to reproduce it in vanilla + CC mod. Simple setup, clones the productivity modules in the machine to module inventory every second.
Steps to reproduce:
1 - place down crafting machine 3, set recipe to gears (or any other that accepts prod. modules), fill machine with prod. modules.
2 - place down crafting combinator facing machine and a constant combinator wired to crafting combinator.
2 - set a value in constant combinator to "Recipe Uranium 238" (I believe any recipe that CANT run on given machine and DOESNT accept prod. modules would work - original was with ores in bob mod)
3 - open module inventory of crafting combinator and watch the productivity modules generation.

Additionally, it would be nice if signals with -ve values were ignored by the combinator; I found this issue by trying to send two different recipes on the same signal and just adding a large -ve to one or the other before sending it to two crafting combinators (expecting each to use the higher value and ignore the lower). Naturally if I dont send any signal the only signal going into the CCs was the -ve 'wrong' signal i was trying to avoid.

For now I just open up the module inventory and lock down all storage (so it just hides the issue), but this raised another thing: copying the configuration of the crafting combinator from one to the other (shift) doesnt copy the number of locked item slots.

Modules have been a real pain throughout this mod, so I wouldn't be surprised if it broke again...

Negative values are accepted by design as it can be useful, but you can filter them out with a simple decider if you don't want that.

TBH, I didn't even realize you can limit the module chest slots :| It's quite possible that it could cause issues with how the mod works atm... I'll have to look at that.

I just tested this and it seems to work just fine for me... It's possible tho that some of the changes in my wip version have fixed it, so I guess we'll see once I release that. As for the module chest limit, it is now copied with the other settings, tho it won't be stored in a blueprint. I want to fix that too, but it's probably going to be a bit more involved and I'd already taken way too long to finish this update, so it'll have to wait.