Thanks for your reply rameez.
I tried this on 2 different systems with different Motherboards and cables.
The port seams to function for normal operations.
I can connect a drive to the secondary master and work with it in windows or dos without a problem.
I can also use tools like MHDD and Victory without a problem.
But when I try to use tool with some SA function, then the drives are showing the Busy register. This only happens with non comercial tools. First I thought It was a bad tool, but now I tried several tools and they all show the secondary as busy.