Ouch! I ran the 10.2.5 update, and was worried about the warning on the update read me when it warned about problems with modified systems. Right after I installed though, I restarted in safe boot and repaired permissions. I'm running Acquisition right now (its core is the same as 2.9.8) with no problems. Any chance you ran into some of the problems expected in the read me?

Post back, and I'll reinstall 2.9.8 if necessary and we could compare.