Hmmm, has it ever happen before? I mean has AmiKit ever worked for you without the graphics problem you are describing?
It might be possible that the problem is in your gfx drivers. Try to update your drivers to the latest version. Also play with the WinUAE Display (or other) settings. More info here: http://www.vware.at/winuaehelp/
If it doesn't help you can always upgrade or downgrade the WinUAE version. Simply search for WinUAE.exe and replace it with newer or older version downloaded from http://www.winuae.net
(the ZIP archives).