In WinUAE select A1200 quickstart config, then add the CF as harddrive and change controller to IDE0. Now check if you still don't get the same problems as on the real A1200.
BTW, run HDToolbox, go to Partition Drive, Advanced Options and Change. There check that MaxTransfer is set to 0x1fe00. Do this for all partitions. If you enter a value into the MaxTransfer field, press enter to confirm it, otherwise the new value won't be saved.
