This is from some notes I found way back when I flashed my card, thought it might help...
The DOS version of sas2flsh requires that the motherboard support the BIOS32 service directory feature. If the BIOS32 service directory feature isn't supported, when DOS is booted and sas2flsh.exe is run, an error message "ERROR: Failed to initialize PAL. Exiting program." will be displayed. You can also use the UEFI version of sas2flsh (sas2flash.efi) if your board supports UEFI.
The BIOS32 service directory support might be available with a BIOS update.
When changing to IR from IT or to IT from IR, a firmware erase must first take place.