I don't know if this bug is in your mod pack or in Bob's Technology mod.
But right now Transport Science Pack can be made only in Burner Assembling Machine and not in other assembling machines.
Please tell me if I should post this bug at Bob's Technology mod page.
During 2.0 save conversion to 2.1 with your pack I have got a warning about some recipes have been removed.
Majority of these recipes were in format maraxix-<science_pack_name>-empty-research-vessel and rf-maraxix-<science_pack_name>-empty-research-vessel. Maybe this has something to do with it.
But on new game start the same problem with Transport science persists.

Hey I am unable to recreate your error, both an old world converted to 2.1 and a current save have transport science available in all assembly machines.

This "Majority of these recipes were in format maraxix-<science_pack_name>-empty-research-vessel and rf-maraxix-<science_pack_name>-empty-research-vessel. Maybe this has something to do with it." was expected as Maraxsis changed so this is separate.

Are you able to give me a list of mods you currently have enabled and a screenshot of Transport Science Pack in Factoriopedia and I can look into it a bit more.

Sure.
The mods that I'm using are
base
elevated-rails
quality
recycler
space-age
aai-containers
aai-industry
aai-loaders
aai-signal-transmission
Accumulator-V2
alien-biomes
alien-biomes-graphics
angelbob-spaceage-rebalance
angelsaddons-bots
angelsaddons-cab
angelsaddons-mobility
angelsaddons-mobility-graphics-crawler
angelsaddons-mobility-graphics-petro
angelsaddons-mobility-graphics-smelting
angelsaddons-storage
angelsbioprocessing
angelsbioprocessinggraphics
angelsinfiniteores
angelspetrochem
angelspetrochemgraphics
angelsrefining
angelsrefininggraphics
angelssmelting
angelssmeltinggraphics
ArmouredBiters-2_1-update
Better_Starmap_Background
bobassembly
bobclasses
bobelectronics
bobenemies
bobequipment
bobgreenhouse
bobinserters
boblibrary
boblogistics
bobmining
bobmodules
bobores
bobplates
bobpower
bobrevamp
bobtech
bobvehicleequipment
bobwarfare
BottleneckLite
bplib
ChangeInserterDropLane
condensing-agricultural-tower
DiscoScience
ElectricTrains
elevated-pipes
enhanced-shadows
equipment-gantry
EvenDistributionLite
FilterHelper
flib
Flow Control
FluidMustFlow
FNEI
helmod
informatron
InserterFuelLeech
item-request-proxy-events
jetpack
kry_stdlib
lamp-post
logistic-helper
LogisticTrainNetwork
LtnManager
LTN_Combinator_Modernized
maraxsis
mineore
module-category-defaults
muluna-graphics
nauvis-cliff-explosives
Paracelsin
Paracelsin-Graphics
planet-muluna
planetaris-arig
planetaris-dyes
planetaris-hyarion
PlanetsLib
pump
RateCalculator
reskins-angels
reskins-assets-base
reskins-assets-bobs
reskins-bobs
reskins-library
reskins-sprite-utils
Return-Inserter
reverse-factory
rigor-module
robot_attrition
SolarMatrix
space-exploration-graphics
space-exploration-graphics-4
space-exploration-graphics-5
SpidertronEnhancements
SpidertronPatrols
squeak-through-2
StatsGui
TaskList
tile-upgrade-planner-muluna
visible-planets
vp-scale
Wr_Enhanced_Map_Colors

I don't know what image hosting is preferred.
I uploaded screenshot of Transport Science from the new game.
https://postimg.cc/2bH0T3qY

Thank you for your time.

Sorry. I missed that you've asked for a screenshot from Factoriopedia. Here it is.
https://postimg.cc/sv2cMzgj

So looking into this, think it may be something with AAI can't recreate it still.

Are you able to run this code and let me know what it says:

/c local r=prototypes.recipe["logistic-science-pack"]; if not r then game.print("Transport Science recipe missing"); return end; game.print("TRANSPORT SCIENCE categories: "..table.concat(r.categories,", ")); for _,n in ipairs({"burner-assembling-machine","assembling-machine-1","assembling-machine-2","assembling-machine-3"}) do local e=prototypes.entity[n]; if e then local c=e.crafting_categories or {}; local match=false; for _,v in pairs(c) do for _,rc in pairs(r.categories) do if v==rc then match=true end end end; game.print(n.." | Categories: "..table.concat(c,", ").." | Compatible: "..tostring(match)) else game.print(n.." | Not found") end end

Then if you also in cheat mode place any assembly machine and see if you can select the recipe in an assembly machine or if its's not visible at all.

Do this in a new save so it doesn't mess your playthrough around.

Thank you

The code returns
Cannot execute command. Error: [string "local r=prototypes.recipe["logistic-science-p..."]:1: <name> expected near ','
I'm not so good with Factorio scripts so I cannot find where the typo is.

You've fixed it already.
The result is
TRANSPORT SCIENCE categories: advanced-crafting
burner-assembling-machine | Categories: | Compatible: false
assembling-machine-1 | Categories: | Compatible: false
assembling-machine-2 | Categories: | Compatible: false
assembling-machine-3 | Categories: | Compatible: false
And no, the recipe for Transport Science is not visible in all assembling-machines except for burner-assembling-machine.
What is more interesting burner-assembling-machine has more science pack recipes, and I'm not sure that they must be there
-Automation
-Transport
-Gold
-Refraction (marked as cannot be produced in this assembler)
-Metallurgic (marked as cannot be produced in this assembler)
-Electromagnetic (marked as cannot be produced in this assembler)

All of this science pack recipes are not visible in assembling-machine-1 and higher, in exception for Automation Science pack. It is visible everywhere.

Okay thank you, can you run this one as well to see what it produces
/c local r=prototypes.recipe["logistic-science-pack"]; if not r then game.print("Recipe missing"); return end; game.print("Transport Science: "..table.concat(r.categories,", ")); for _,n in ipairs({"burner-assembling-machine","assembling-machine-1","assembling-machine-2","assembling-machine-3"}) do local e=prototypes.entity[n]; if e then local c={}; for k in pairs(e.crafting_categories or {}) do c[#c+1]=k end; table.sort(c); local ok=false; for _,v in ipairs(r.categories) do if e.crafting_categories and e.crafting_categories[v] then ok=true end end; game.print(n.." | "..table.concat(c,", ").." | Compatible: "..tostring(ok)) else game.print(n.." | NOT FOUND") end end

Transport Science: advanced-crafting
burner-assembling-machine | burner-crafting, crafting, electromagnetics, metallurgy, parameters | Compatible: false
assembling-machine-1 | advanced-crafting, crafting, parameters | Compatible: true
assembling-machine-2 | ab-aquilo-washing, advanced-crafting, crafting, crafting-with-fluid, parameters | Compatible: true
assembling-machine-3 | ab-aquilo-washing, advanced-crafting, crafting, crafting-with-fluid, crafting-with-fluid-and-data, parameters | Compatible: true

Could you please add file output to the script if more tests will be needed?
I've done it myself for this command, but I'm not sure if all is correct.
But the output in file corresponds to the output in game.
Or is there a way to copy console output in game? I don't know any...

Hey, thank you for responding, you can get all the chat logs from the factorio log in the installed file location (Normally Appdata folder). Sorry thought you were getting them from there. I am just writing the code that will hopefully fix the issue.

Ok. I'll look more closely next time for logs output if Appdata folder.
This means that you've figured out the cause of the problem?
I'll be waiting. Thank you.

I have hopefully fixed this please let me know if it is patched in 1.3.1.

Yep. All fixed.
Thank you for the fast fix.