as far I can test, IE, botania and TFC are some examples.
Tool restock works normally with just quark

UPDATE:
this is the list of mods I can narrow where this happens: modlist
latest log: latest.log

Removing any of those mods makes the feature work, as far as I can test.

After some more tests I noticed it's not fault of those mods but the combinations of any of those (an possibly others) with some performance mod (I assume?).
Just quark + botania (as example), the restock works.
just quark + a bunch of performance mods (I'll try to narrow the list of culprits later), restock works
quark + botania (or any of the other listed in the post) + performance mods, restock breaks

Updated the issue, couldn't narrow it more, good hunting team

doing more testing I got part of the problem, whatever mod is breaking this, is triggering this check and making tools not restock

So I narrow it down to a Zeta registration? problem (which makes sense since I'm pretty sure this was working at some point in my personal pack)
The problem seems to be here, this runs twice at the start of the pack, in a working tool restock condition, the first time it runs the manager variable is empty, and the 2nd time it's filled (as you can see here).
In a non working condition it runs twice but it's inverted, first time manager is filled and the 2nd time is empty, which also empties flagManager & sortedFlags (as you can see here)
I am not sure why, how, or who... so, good luck Zeta warriors.