Sorry can't help you..
I also have problems with my Kickflash. I have an A4000 (with Apollo4040) with Towerhawk 7 slot bus board. And 3.0 real ROMs.
I tried flashing the Kickflash with 3.1 roms and 3.9 rom update. I can't get it to work (i removed the jumper on the card). But computer still shows the version number of the 3.0 ROMs. Do i need real 3.1 ROMs to be able to do this?