Hi Stephen and thanks for your interest in AmiKit.
There are more similar reports (random freezes) and it seems it happens on Dualcore CPUs only. Do you have such a CPU?
There's WinUAE 1.3.2 included in default AmiKit installation. You might want to upgrade to WinUAE 1.3.3 because it contains "Dual core directory filesystem freeze workaround".
Simply download WinUAE
archive and copy WinUAE.exe into AmiKit\WinUAE\ folder.
There's also newer version of WinUAE available (1.3.4). The change log says: "Windows Vista compatibility problems fixed" and "Dualcore/SMP random freezes properly fixed". However this version also contains a bug which ignores relative paths set in AmiKit. This might prevent AmiKit to start on certain systems.
If newer WinUAE versions do not solve your problem, you can always disable "JIT" option in WinUAE/CPU settings as it might be the source of these random freezes. Run AmiKit GUI, press the "Configure WinUAE" entry, disable JIT and start the emulation. However, the emulation becomes VERY slow without the JIT.