What Guru error number do you get? What version of Workbench is on the IDE Hard Disk? Also, what filesystem is DH0: and DH1: on the IDE Hard Disk formatted as? That said, I'm doubting it's the RDB that's causing the issue in this case.
If you are running any hacks/patches in your S:startup-sequence, try to disable them by booting with no startup sequence from the early startup menu and running a text editor like 'ed' on the file or booting from a WB floppy and doing the same. It would appear that it's hitting something at the top of your startup-sequence that's incompatible with the board. Then, use the process of elimination by slowly introducing each hack/patch back until you get the guru. It's good you have possibly eliminated the Deneb as a cause, though what is installed on its flash?
Also, try running a different 68060 library like the MMULib version to see if that fixes it if the above did not work. I'd also suggest using the latest GVP 68060 library as the one on the supplied floppy may not be the latest if I recall.
Also, try booting with jumper JR1 disabled (Burst mode) to see if this makes any difference. In my experimentation with memory on the A4060DT I've found certain memory SIMM combinations will POST fine but crash the machine while booting with this jumper enabled if not all the RAM is up to this mode. Software Hut supplied me with 128MB with the A4060DT I bought (and since sold), of which only 2 of the SIMMs would correctly function in Burst mode.
