I have the same issue as OP! Also as per this thread https://forums.beamdog.com/discussion/77637/fighters-not-receiving-apr-bonus-at-level-7. The component is broken on BG2EE, but it's working fine on my BG1EE install.
I took a nose about in NI as subtledoctor suggested in that thread and could see what was wrong, but not why or how best to fix it. My working BG1EE version of CLABFI01.2DA (and the other relevant class tables) has a row for AP_D5_NUMAT to be applied at levels 7 and 13 as expected. On BG2EE that row is missing for some reason, so nothing ever gets applied and they sit at 1 APR.
I can't reinstall to fix this without ruining my savegame thanks to Item Randomiser being installed. Also, I don't know if these tables are used by enemies at all, and I don't want to gimp SCS enemies by mistake.
So should I copy the CLABxxx files from my working BG1EE install over the broken BG2EE versions? Presumably this won't retrospectively fix things for my >7th level characters, but I can then use EEKeeper to copy the effects from a new character or something similar?
Attached weidu logs and comparison of the 2da files.
bg2_broken_WeiDU.log
bg1_workgin_weidu.log