The BIOS option ROM space is a limited resource and your machine has run out of BIOS option ROM space. The Qio BIOS takes some of this space to do the PCI bus re-arrangement and to enable hot plug. You must free space by disabling one or more unused option ROMs in BIOS. For example, you may disable a large option ROM, like the LSI RAID controller (exists on many motherboards but is rarely used.)
The ethernet ports have been re-assigned new port numbers by Windows and do not have the previous settings. Any ethernet-specific settings must be reset in Adapter Settings. Sonnet is investigating this issue.