The bug had to do with the fact that somehow the required version of the .NET Framework has been reset to 4.0 just before I released it. As a result, if you had a project with .NET Framework set to 4.0 everything would work as expected. For all other framework versions, you would get an error saying that the MaventionMinifiedJsFileGenerator, MaventionObfuscatedJsFileGenerator or MaventionMinifiedCssFileGenerator (depending on which one you were trying to use) custom tool was not found on the system. Paul Schaeflein came up with with a fix for this bug which was as easy as changing the minimal version of the .NET Framework to 3.5.
I’ve just published the new version of Mavention SharePoint Assets Minifier (v1.0.1) to the Visual Studio Gallery and if you have the extension already installed, you should automatically get the update via the Extension Manager.
@Paul: thank you very much for the bugfix suggestion!
Download Mavention SharePoint Assets Minifier from Visual Studio Gallery.