if memory servers me correct, if you add any ship that replaces an AI file (including BasicAttackAI, BorgAttackAI, QuickBattleAI and others that i can't think of off hand) you run the risk of screwing up the BorgAI in KM and possibly other AI's as well. Im not sure if any changes were made in the AI files from KM0.9 to KM1.0. but as far as i could tell when i install KM1.0 after release, everything worked fine with the Borg the exact same way it did with KM0.9 so i didn't even bother to check. your best option is to replace the AI folder with the original one from the KM1.0 mod. and for future reference, whenever adding new mods to KM, never overwrite an AI file. files in the AI folder are sometimes dependent on others to function properly, especially the BorgAI and PlayerAI.
jayce - aka. Resistance Is Futile - creator of PlayerAI and BorgAI in KM with the some assistance from Defiant