In FlashSPI use the /X or /Z switch, must be capital letter. Be sure you are using the latest FlashSPI that came with the newest BIOS you have
So try
A> FlashSPI BIOSfileName.Fxx /X
or
A> FlashSPI BIOSfileName.Fxx /Z
If that fails try /F switch instead (Above are both force too, but one will flash BIOS BIOSes at once) If you do use the /F switch BE SURE you have the correct version of BIOS for your version of motherboard (IE Rev. 1.0 BIOS for Rev. 1.0 board, 2.0 BIOS for 2.0 board, ect.)
It does sound like maybe this memory is bad to begin with, or incompatible with the board, since you could never get it booting at the correct speeds. Can you test with other memory to rule this out? DDR3 is dirt cheap these days, so have a look around for a single 2Gb or 4GB module for testing, you can probably find a 2Gb for under $20 and a 4GB for around $20-25