Base THAC0 for thief and bard companions seems to be too low.
For example Nalia has 11 THAC0 at level 9, Imoen 12 THAC0 at level 8, Haer'Dalis 9 THAC0 at level 10.
Reproducible for me with just:
~STRATAGEMS\SETUP-STRATAGEMS.TP2~ #0 #5900 // Initialise AI components (required for all tactical and AI components): 35.1
~STRATAGEMS\SETUP-STRATAGEMS.TP2~ #0 #6000 // Smarter general AI: 35.1