The BMS (PA31) pin is sampled at powerup to determine if the chip boots from parallell flash or the internal bootloader. I suspect that the CSB337 has PA31 tied low - thus booting from the parallel flash. (Looking at the specs for the CSB337 - I see no dataflash, no EEProm, or 8-bit parallel flash - therefore the on-chip bootloader would in all likelyhood not be used on this board)
If this is the case - then disabling the CS for the flash will have no effect, except to make the board hang....
What you need to do is determine how they pull PA31 low - if you have the schematic that should be easy - or maybe their tech support won't mind telling you.
PA31 and PA30 are the TX and RX lines for the debug serial port. Again you will have to find out if these signals are available, either as one of their two standard serial ports, or in the GPIO header.
What you need to do is find the PA31 siganl and pull it high - then you can confirm that the on-chip bootloader is functioning if you received a series of 'C' s out of the config port (115200 8N1) after powerup.
(a side note - if the AT91RM9200 are rev 1 chips there will be NO on chip bootloader. Rev 2 chips should be marked with 58A07F in the bottom left corner)