I'm having a bit of trouble with a lc550 board I've put into a colour classic.

The problem is that I always get the error that I have not shut down my computer correctly - this also seems to trigger some sort of disk check that makes it take ages to mount the partitions I have (so turning off the warning isn't a solution).

I've tried deleting the finder and general controls prefs and the battery is new and working fine otherwise (and I've tested it with a multimeter).

I get the feeling this is a software problem.. but I'm at a loss to what it exactly is. Any thoughts?