If you run a Cygwin application as a service in Windows (using cygrunsrv), you'll have to make sure the application (and any data files it uses) have correct permissions. Start at 777 and test if you're unsure.
Also make sure the path is correct. Mixed Cygwin/Windows apps act really freaky when it comes to paths. This includes both using the Windows and Cygwin path as using the full Cygwin path to an app and assume that the PATH is not exported by default.
Export any environment variable by passing the -e parameter.
