You do lose considerable functionality by completely disabling the ROM Update (31KHz bootmenu, scsi/ide upgrades, FFS upgrades, etc). If you're willing to do more testing, you could try disabling individual modules from the update until you find the one responsible.
My first guess would be exec.library, so try using
C:SetPatch SKIPROMUPDATES "exec.library"
Or you can deal with the extra reboot by not disabling anything. It's not too bad, and you get used to it ;-)