It seems that earlier version of WinUAE have problem with dual core CPUs that results in random hangs of AmiKit during its startup or shortly after. Please download and use the latest version of WinUAE
to fix the problem. It is enough to copy WinUAE.exe to AmiKit\WinUAE\ directory. Another solution is to disable JIT in WinUAE/CPU settings - however the emulation will be very slow without JIT.