Hi there,
This sounds like it could be a maxtransfer issue. When using CF Cards on A600/A1200s IDE Port, if the maxtransfer value is set too high (in HDToolbox) it can cause all sorts of odd probles. It's down to CF Cards not being happy with transferring large blocks of data at once, so you need to set a fairly low value. Try changing the maxtrasfer to 0x1fe00 then save and reboot, see how it goes. Changing this setting will not destroy your data or result in slower transfers so it's worth a shot

Hope it works!
Robert.