The fact you can open your hard drive with the right mouse button boot to pure Workbench makes it sound like a Scalos issue. Perhaps that's why other preinstalled Workbenches work - they don't use Scalos.
I just can't understand why it would only affect your machine. It would seem like a CF setup issue; I doubt your adaptor is faulty.
I'm not familiar with setting up CF cards and you've explained that you've tried a smaller one with the same result. You said what the maxtransfer value is - what about the mask value? Also, your maxtrans value seems strange. Look here:
http://www.xs4all.nl/~hjohn/SFS/maxtrans.htm
It would be useful if you could test a real hard drive, then we can at least try and identify the cause.
When you go back to your adaptor, can you please try and disable FBlit:
under the menubar Settings->FBlit->disable
or
Launch/Buttonmenu Settings->FBlit->disable
then try.