I had the same problems at about the same time that Wings first posted the list but I was using an HCS08GT32 and was able to switch to a Softec inDART debugger that didn't have the same problems. Now I am using an HCS08GT16A processor with basically the same code and board and the inDART won't connect. I suspect they don't support the A version but I have gotten no reply from them on the subject.
I am suprised that P&E/Metrowerks woulden't have fixed bugs from a year ago but I have downloaded the latest P&E drivers for the Multilink and I don't see any hardware upgrades available on their site.
I am using the simplest clock setup - fixed 4 mHz - no FLL - 1 mHz bus. Any suggestions would be greatly appreciated.