So you used `cogspur\Squeak.exe Cuis5.0-4426.image -s ../scripts/setUpEnvironment.st` on Windows. I don't know where path normalization kicks in, but what about `cogspur\Squeak.exe Cuis5.0-4426.image -s ..\scripts\setUpEnvironment.st`?
Also, in the past, the script sometimes needed to be an absolute path, maybe try that too?