The following seems to happen only with AMD processor motherboards. I detected the problem with Gigabyte GA-7N400S and GA-K8NS so far, maybe other boards with AMD processors are also affected. It seems that boards with Intel processors are not affected. I could also see that the problem seems to be related to some kernel-version specific things but have no idea which module exactly.

I've tried to use the following distributions / versions:
Suse-Linux  9.0 (kernel 2.4)      - no problem
Suse-Linux  9.3 (kernel 2.6)      - wakeup does not work
Suse-Linux 10.0 (kernel 2.6)      - wakeup does not work
Fedora core 1 (kernel 2.4)        - no problem
Fedora core 5 (kernel 2.6)        - wakeup does not work
debian sarge (kernel 2.4 and 2.6) - no problem
knoppix 5.0 (kernel 2.6)          - wakeup does not work

It is definitely no hardware problem. The boards have been checked by the manufacturer (german service center) an are working without any problems.

The problem is - if I use one of the 'not working distrubutions' - a simple run of this operating system destroys the bios data and the machine (almost) never wakes up. But if I clear the cmos data and set the needed values again the machine will wakeup again - only one times.

The problem is so important for us because many of our maintenance operations are based of this feature and there is no simple way to use another technology for these things. Until now all effected machines were running (for compatibility reasons) with Suse 9.0 but now we have to switch to 10.0