I set up an ambush in my hack alone and didn't run into that bug.
I got IPS Peek and FF Restored to check if there's any overlapping changes. There are some.

The two big blocks are dealing with poison and regeneration. I don't know what Restored is doing with it. In my hack all the EAs are there to remove the code that loops through enemies, so that it only performs the regen/poison on one entity.
Above that might be the problem. It's just a one-byte change, but...
In mine:
LDA #$00
STA btl_strikingfirst
If FF Restored is overwriting just that one byte? It's not setting btl_strikingfirst to 0 after a round, but some other variable - one of the characters' battle stats.
It also changes 000323FF to $82 from $D0. That's part of the "try to run from battle" routine, I don't know what that might mess up.
What order did you patch it in? Like I said before, I don't really know what happens when you put two patches together, but if you put Restored first, then this one, maybe this one will overwrite the changes Restored does? However, even if it does, the poison/regeneration stuff will be messed up, because then my hack will just be scribbling all over the much larger edits Restored did to those routines.
I'd suggest making two patched roms then:
On one rom, patch Restored on first, then this hack.
On the second rom, patch just this hack.
Then edit them both in a hex editor. In the second rom, copy everything from 000321E8 to 00032340 and paste it over that area in the first rom.
That should fix the striking first flag not being set to 0, as well as making sure poison/regen doesn't go wonky.
And then make sure 000323FF is set to $D0 maybe.
Actually, that $82 is important, but its shifted over 5 bytes. 00032404 should be $82 instead of $80, to fix the running bug--
; The problem is... the game is BUGGED and reads the wrong value for the level.. it ends up reading
; the ailment byte for 2 players after this one (for top 2 slots) or other garbage memory for the
; bottom 2 players.
Hope that's not too confusing to try!