I've revisited the BE6 board recently and found some more information.
Does the "Safe scan of potentially problematic PCI devices" options use a list of known problematic PCI devices or will it "Safe scan" all PCI devices? Because I found, that this PC will always hang if I poke specific PCI registers on the PIIX4E Power Management Controller (8006 7113). I've made a simple batch file and tried to read with PCISET every register from 00 to FF and it would hang around the C6-CF registers. These are "reserved" according to the Intel datasheet and it looks like on the Abit board they "bomb" if touched.