My Amiga Technologies A4000T has always done exactly the same thing.
Like you found, it only does it when there are IDE devices present.
Doesn't worry me much as the computer runs 24/7.
Never really looked into the problem in detail, but it appears to be some kind of timing issue as it accesses IDE devices during boot.
Changing SCSI spinup time or whatever doesn't fix it either. You'll be running OS version 40.70 which is OS 3.1 with the A4000T SCSI controller software and without workbench.library.
Possibly the way to fix it properly would be to edit the code in ROM to change how things are done during boot, but that's not so easy without a copy of the source code handy :-P
