I've had this exact same problem too when I installed some system enhancers too.
In the end I had to use my backup to restore the system. I never found out what it was. it was one of the utils mentioned in the OS3.9 enhancements topic (Amber RAM maybe?).
I guess some of the utils patches a library or some other system file because commenting out startup-sequence items or disableing WBStartUp didn't work for me either...
