Using the latest WebCore (2.9.8.0), the TMSWebCompiler.exe (Version 1.9.0.0) obviously no longer regards the “Version” command line switch to extend the naming of the .js file. It always takes the version name from the project file, but not from the command line parameter.
As far as I can see, in Compiler Version 1.6.0.2 (included in WebCore 2.5.4.0) it still worked.
As my reloading mechanisms (for updated .js files) rely massively on this, it is very important for me to get that fixed.