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Hi
The stock FC5 kernel probably doesn't have a driver for some component on your motherboard (guessing here) or for the motherboard chipset. This can happen, especially if your mobo is very new (which it seems to be, from your post?)
I got this type of behaviour on a an older 3.2 P4 Xeon machine a friend brought in the other day (don't remember now which motherboard it had, or from whom). The partial solution was to recompile the kernel (on my own FC3 system) and then swap the kernels around on his, trying different drivers with each swap. I had the same problem that sometimes it wouldn't boot, and if it did boot, it was very slow.
The slowness is most likely 'cause DMA is not working on the board, due to there not being a chipset driver for your chipset in the stock FC5 kernel. I had this with by GA8TRS350MT mainboard - the stock FC3 kernel worked, but it was -slow- because there was no kernel driver for the ATI RS350 chipset I had on the board. So I downloaded a newer kernel which DID have the chipset support in for my motherboard (2.6.14.3) and compiled that and got DMA working.
I realise you do have a problem if it won't even boot (sometimes) but you might try to see if there is a newer kernel version around than the stock FC5 kernel (I'm guessing that there is), and also try to see if you can find a chipset driver for your chipset specifically.
I found mine by searching through the kernel config file, and then enabling a few lines that seemed to refer to my RS350 / ATI IXP chipset.
Hope this helps!
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