It could be timing with the flash. Try a different CF with DMA to see if that works. WinSystems (http://www.seanliming.com/flashhelp.html) has some CF cards with DMA support.
It could also be a faulty driver. Please make sure you have the latest drivers for the system.
Also, PC104 has some peculiar characteristics. If you stack the PC104 cards in different orders the results will be different. This is a cause of the capacitance loading on the bus.
-Sean