What file system are you using on your hard drive?
I've seen this lately with PFS2, it usually means the media my boot partition sits upon is starting the slide to oblivion. My SCSI drives are rather old. I've had to re-think the way I organize and protect data. For your sake, I hope I'm wrong.
Do you have backups?
AFAIK the file system is SFS. I bought my A4000T from a friend of mine and i believe that he had formatted it as SFS. I never touched the formatting as if i remember right it already had a fresh install of OS3.9.
What i can say is that when the problem started (Attempting to load program WBCLOCK) i would reboot or else switch off and on again and the problem would go away and it would load up properly. It started this about a week ago. I thought the problem had to do with a failing Clock battery.
Yesterday when i tried rebooting or off/on again the problem remained and now my OS3.9 installation is what one can say totally unusable as it freezes as soon as the "Attempting to load......" thingy comes up.
Should i try renaming the WBSTARTUP folder to something else and see what happens or is there something else i can try?
I have another partition with Workbench 3.1 on the same hard drive. Should i try booting with that instead and use some tool to fix 3.9 ?
Any help would be appreciated.