If I just click on the exe I get a Cygwin1.dll is missing error...
Copying the missing library from any Cygwin package (installed or not) into the SplitFus executable folder should solve the issue...
a bit prettier way to add x:\cygwin\bin to your windows PATH environment var
and the you can run SplitFUS2 via Windows CMD.
I'm not sure it solves thom80's issue, but give it a try