Some updates on this problem:
I contacted the MSI support, which was quite disappointing since they dont seem to be very experienced in Linux support. They even admitted that they did not test with Linux

So I will keep bothering you
I installed a new Bios version, but with no improvement.
My current setup:
- Bios version: 1.4
- Linux kernel: 2.6.19.2-amd64
- Nvidia driver: 9746
I can reproduce the freeze very fast ( < 5 min) by playing Warcraft III with wine.
But also the SPECViewperf Benchmark results in the freeze.
However I was only able to reproduce the problem in my 32Bit chroot. So maybe there is something wrong with the 32Bit libraries.
<edit>I was able to reproduce the problem also in the normal 64Bit environment. It just takes some more time...</edit>
I also tried a new kernel version 2.6.20-rc4 without success.
And in addition I bootet the kernel with various combinations of
noapic,
pci=noacpi and
pci=biosirq, but the freezes still occur. I thought that these options would circumvent Bios problems?
I you have any ideas how to debug this problem, I would appreciate this!
Regards,
Markus