IP35-E has ICH9 so no RAID
IP35 has ICH9R (so Intel Matrix RAID), firewire, different chipset cooling, solid caps around the CPU
IP35 Pro has ICH9R, firewire, different again cooling, all solid caps, dual Gb LAN, 2nd physical x16 PCI-E slot (x4 electrical), 2x eSATA, external clearCMOS switch, uGuru
They're all great boards & yes, the beta BIOS fixes the IP35-E/IP35 double boot.
topher, if you got an Asus or a Gigabyte you would probably want to flash the BIOS on those too as there will have been improvements since the board was shipped from the factory.