Issue with JEI autofill of Patterns

[xJon]

Describe the bug
First reported over xJon/The-1.12.2-Pack#990, I can reproduce the issue with all of the versions of AE2 Unofficial Extended Edition I tested.
Changing to the normal (old) edition (rv6-stable-7) resolves the issue.
I am unable to reproduce the issue with just AE2 Unofficial Extended Edition installed, so I guess it is an incompatibility with one of the mods in The 1.12.2 Pack, but I was unable to figure out which one.

To Reproduce
In The 1.12.2 Pack, since version 1.5.0 a couple of years ago when it changed to AE2 Unofficial Extended Edition:

1. Setup an auto-crafting process for a Fluix Seed, and an auto-smelting process for a Pure Fluix Crystal.
2. Request a Pure Fluix Crystal - it should work
3. Restart the game fully, and try again to request a Pure Fluix Crystal - it should not work, showing this:
   
   And requiring you to re-create the Fluix Seed auto-crafting Encoded Pattern.
   If alternatively you want to auto-craft Fluix Seeds directly (rather than through the Pure Fluix Crustal process), there is no issue:
   

Any input would be appreciated!

[xJon]

Upon further testing, it seems that manually inputting the items in the Pattern Terminal - and not utilising the HEI auto-fill - prevents this issue from happening. Strange... I guess it is not an AE2 issue directly, then?