(Just a little update for those with a similar problem..)
The mainboard is a Supermicro 370DL3. I figured out that my problems 
could be solved with ACPI (there is a kernel option concerning acpi and 
interrupts). Unfortunately a kernel with ACPI enabled will crash on 
boot. Funnily enough it still manages to switch off the system with acpi 
when pressing the power button.
I have the DSDT lying around here because i was able to dump it with 
FreeBSD previously (in the short time FreeBSD with ACPI enabled wouldn't 
crash..) but i don't how to fix this:

acpi.asl.org   278:     Name (IO, 0x01)
Error    1037 -                ^ syntax error, unexpected PARSEOP_IO, 
expecting PARSEOP_NAMESEG or PARSEOP_NAMESTRING

acpi.asl.org   279:     Scope (IO)
Error    1037 -                 ^ syntax error, unexpected PARSEOP_IO, 
expecting PARSEOP_NAMESEG or PARSEOP_NAMESTRING

At the moment i'm not very keen on crawling through the ACPI 
specifications and get into that stuff just to find out how to fix this.
Whatsmore i ain't got the time at the moment (exams..) and i'm too 
frustrated about that so i'm likely to install FreeBSD.

Let's hope that with the growing popularity of open source software 
hardware manufacturers will someday build standard compliant hardware..

Best Regards,

Jochen Keil