Ok, then please go back to WinUAE.
On the Quickstart page select an A500 with 1 MB Chip RAM and move the compatibility slider to the rightmost position. If "start in quickstart mode" is disabled click on "Set Configuration".
Change to the Adv. Chipset page. Untick "compatible settings" and add A600/A1200 IDE. Do not change anything else.
On the ROM page select "KS ROM 3.1 (A500/A600/A2000)".
On the RAM page move Fast to 8 MB.
On the harddrives page click on Add Harddrive and select your CF card. Change HD Controller to IDE0 and tick Read/Write. Then click on Ok.
If you start this configuration, does it boot correctly or does it give you the same "not a dos disk" message?