Strange...
Do you have a proper IDE splitter and software? If you do, the new scsi.device in OS3.9 may be causing trouble.
Elbox (and some other) splitter software installs it's own scsi.device replacement which is made resident after a reset. OS3.9 also tries to make another version of scsi.device resident after a reset. This might explain why the problem is intermittent.
Change the Setpatch line(s) in your s:startup-sequence to read something like...
Setpatch QUIET SKIPROMMODULES scsi.device
(might be SKIPROMUPDATES actually, but should be right.)