@Framiga:
Thanks for the tip, I tried removing the UnitControl stuff from my Startup-Sequence and guess what - the settings were still the same. The same ones that I have set in the bootmenu even.
To make a long story short. Once upon a time when I evidently had some bad cabling/termination the bootmenu settings for synchronous and frequency did never seem to have any effect, thats why I tried using UnitControl once, forcing it to synchronous mode and making the computer unstable when accessing the harddrive

.
When I got good cables and termination and felt good to go with synchronous mode, I just threw the UnitControl stuff back into the Startup-Sequence again as I didnt think the bootmenu stuff really worked.
Now it struck me that the reason it never seemed to care for my settings earlier was because the card/firmware probably senses if the cabling/termination is working more or less ok and doesn't activate synchronous mode for you if it is not ok.
Moments like this makes you feel a bit... ahem.. not too smart ;=).
/Patrik