Ope found it in scripts>base items, gonna see if i can get to the root of this myself, i can't imagine it would be any mod conflicts though because I only have this, ORGM and a ORGM to Hydrocraft patch

Okay here we go with the next weirdest thing:
I made a baseball bat w/ wrench, a HC item, and that's not getting the references to hc items like glue jars? To double check it wasn't a conflict i disabled e verything but hydrocraft, so this is downright confusing.
https://i.imgur.com/WbONoCS.jpg

https://i.imgur.com/XofKza2.jpg In this you can clearly see I have Packing Tape in my inventory but it doesn't show up in the repair menu.

Removing the hydrocraft. prefix seemed to have worked Still shows as a 'file name' kind of item, but it's linking correctly now at least to the packing take/masking tape item

https://i.imgur.com/U6tSD4m.jpg
https://i.imgur.com/d8rqtdx.jpg

This hsould now be fixed it the updated I just released.

Hydrocraft items seem to be fixed, but the base items are not.
https://i.imgur.com/esAN0rU.png
https://i.imgur.com/IkoIiA5.jpg

I'll play around and see if there's anything I can figure out.

Mirroring from forums so people don't get lost:
gg me
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Wow okay that was a thing

I moved the baseball bat fixer recipe into scripts>weapons bats and all the references worked. 
https://i.imgur.com/mTaTQ9u.jpg

Then I removed the fixer stuff from scripts>base items

Also might I say that not having to make a new save every time I reload sped this up so much, i was making new saves and hunting for packing tape last night every time lol.

https://i.imgur.com/0vrNM47.jpg
(Changed in >weapons bats)
https://i.imgur.com/KtiRcv3.jpg
(removed base repair items from the >weapons bats entry

Afterwards everything worked, but you might wanna remove the basic repair recipe stuff so it doesn't repeat itself. Maybe you could do multiple entries if you're changing a base item's repair cost, one in scripts>base items and then the hydrocraft additions in scripts>'weapon file'?

^^^ After testing this I can verify that it works and I appear to have solved the problem of base items not playing nice with hydrocraft items. You can remove the hydrocraft prefix and it'll work, but with a weird file name, or you can have an additional entry within a hydrocraft file, as well as an entry in the base items file if you're needing to change any fixing costs from the base game.

https://i.imgur.com/5FnbJ3K.jpg
We gucci
https://i.imgur.com/SPNOxRc.jpg

Its because i fogot about the base item recipies. I will fix them in the next update.

Updated to fix. let me know if you find any other item repairing problems.

looks to be working, however
https://i.imgur.com/40gJuWe.jpg
original repairs reqs are repeated, looks like you just needa have the hydrocraft repairs in the scripts>weapon bats entry.

Nice! Thanks for reporting. Will remove the redundant fields next update.

I love how active you are with this mod, Hydromancerx! Honestly, this helped to sell me and a couple of my friends on subbing to it recently.

Thanks! Let me know if you run into any problems.