Hummmm, ermmmmm, ahannnnnn......
What exactly ROM do you have? 3.0?
If is, that's maybe the cause of the missbehaving. You reboot from hotreboot (CTRL+A+A) or coldboot (turn Amiga off, wait and then on again). Maybe the hd lost the RDB in every time you reboot, then the 4000 try to re-validate the hd.
Or maybe your old HD is going bad. It happened to me once with an IBM 2.5" HD. Partition, fine. Formatting, fine. Installing, fine. Play with it for 4~5 hours, fine. Turn off Miggy, in the other day the hd is totally lost/trashed.:pissed:
Try with another hd, maybe this is the cause of your problems.....