Yes - certainly worth disabling the bus boost for now. I remember that being a bit temperamental when I had a CT60. The CT63 doesn't have the integrated bus boost and now I use a Phantom instead - seems solid.
Having to reset a few times before successful boot-up is also something I recognise from my old CT60 as well - although I did find a sweet spot with the clock but can't for the life of me remember what I set it to - CIH now has that machine, he may be able to chime in and remind me.
Anyway, I digress, do you know what rev 060 you have? are you using CTCM or a regular crystal? What speed are you running the 060 at? What RAM are you using? What is it's rated speed?
Did you remove J7 from the EtherNAT??
Do you have a CTPCI? If so, you must also remove J7 from the SuperVidel.
Have you tried using NVDI? This will disable the Falcon's blitter which can't be snooped by the SV (admittedly, this is a bit of a long shot).
If you can get to something 'safe' like:
Run 060 at it's rated speed (check your 060 to be sure)
Use PC133 CS=2 unbuffered SDRAM (check here: http://www.powerphenix.com/CT60/english/sdram.htm
Switch off the F030 boost
Remove the EtherNAT.
In fact, remove any peripheral that isn't crucial.
I know this all sounds a bit overkill, but sometimes you just need to strip it all back to something that falls well within safe boundaries, get stuff working then start pushing things until something wheezes before winding it back a bit to get somewhere optimal and robust.