hello. So, if I understand you correctly, after the BIOS change, the system errors out whether it's booted cold or warm? And, the errors are the same, that is, yu're getting cmd timeouts?
So, what are the BIOS options related to APIC handling? Also, you might try building a kernel with options PCI_INTR_FIXUP to see if that changes the way interupts are routed on the system. -thanks -Brian