Hi Knut,
this is a problem I ran into multiple times since I've been working with FPGA based HTX boards now and it appears to me there is - as always - no general way to fix that issue. It all depends greatly on the mobo setup. Hard reset isnt always behaving as you would expect. An HT link reinitialization only takes place if either pwrkok goes down (the cold reset case), or ldtstop forces the link into idle state (which most Opterons out there dont seem to support yet). Additionally, almost every mainboard vendor ignores the fact that powerok and reset_n on every HT link is defined as bidirectional. I am working with a Tyan S2912 with fam10 cpus, and its MCP55 seems to control abovementioned signals unidirectionally. If this should be the case with your board, too, there are two possible ways to fix your issue. If you have the southbridge documentation and it truly controls all HT sideband signals, implement your own, real hard reset. Another thing that works on some boards (e.g. on Tyan) is pressing and holding the reset button before pressing the power button and letting it go sometimes afterwards. This holds the southbridge in init state and leaves your card all the time you need to have it program itself.
Good luck and best regards,
Maximilian Thuermer