Hey! so you were on the right track with the 2v2 mod being the issue, and I haven't had too much testing with it but it seems to be working fine now; it was the Pokebattle_Battle script of the 2v2 mod not including many of the changes of AllGen's. I'm not entirely certain of the rules regarding posting another mod's scripts with 1 very minor edit, so in case @Fervis is opposed to other people sharing AllGen's scripts, you can do the edit yourself very easily; In Pokebattle_battle, theres a script for "Initialize battle class" and under it there is line called @doublebattle set to false, so just set it to true. It seems to be working fine for me albeit I haven't extensively tested it yet. Hope it helps dude!
Edit: Lol I posted this too early, there seems to be other changes to that script that the 2v2 mod made that I haven't caught yet; I'll give an update when I catch them all
Edit 2: Ok so I found the culprit script, but permission wise its even more muddy than the last change but in Pokebattle_battle, the 2v2 mod also changes the script for "Initialize opponents in double battles", so I just replaced AllGen's scripts for that function with the 2v2 mod's. (From what I understand, the 2v2 mod's script is for when trainers only have 1 pokemon); I won't share the patched file unless I get permission from both @Fervis and @Vilrose. Cheers!