After 3 houers of google grinding i have finaly found a fix to my problem.
I just had to add: NoCache in the whdload pref list and chaos engine runs superb (still a litle slowdown when alot of explosions are happening)
Setting the "NoCache" tooltype usually fixes problematic games on the '060, as you found with the possibly of some slowdown. Interestingly, the type of accelerator seems to have some influence. Here, the title music of SOTB3 is slightly out of sync on both the TekMagic and Apollo '060's, but it's perfect on the MKII. Tooltypes have no influence.
One WHDLoad niggle I've never been able to solve - Moonstone. A voice drops out of one of the audio chanels while the game loads, never to return. This happens even on my little 600/030. :/