Well when I got a SCSI-IV kit for my Blizzard 1260 I read that the 3.1 ROMs would increase boot time by 10s. This was because the newer ROM would scan all buses and wait longer for the IDE interface to respond (slow spinup drives).
So it's possible the ROM is causing a conflict but I doubt it's something you couldn't patch.
What is Dawn Patrol anyway? Do you have a 68881/68882 to '060 program like Cyberpatcher/Oxypatcher?