I have the same board and I haven't had any problems with the EFI firmware except for a bug where USB would fail to initialize if my SideWinder X4 was plugged in. I called them and within 24 hours, they gave me a beta firmware to fix it. What firmware revision did you flash? I'm running 1.J (1.19) dated 3/7/12 which is actually a later version than they have on their website which is 1.I (1.18). I really don't trust a software flasher like Live Update. I use the M-flash tool in the firmware itself to do the updating and I've never had a problem with a bad flash. One thing I do notice on this board is that an EFI change will reset you to defaults, so you may want to check that your SATA controller is still in AHCI mode if it was before.
EDIT: One trick I've learned with this board is that you can actually use the overclocking profiles to preserve your whole configuration, not just overclocking settings. It will preserve VT-x settings, PCI latency, HPET, boot priority, SATA mode, RAID, ACPI settings, all sorts of stuff.