I am running version 1.5.0.0, so maybe a more recent version takes care of this.

Drag an audio file to the RMS from FolderA in Windows Explorer. Edit and save the file. It is saved in FolderA (that's good). Use the Open Media File command to edit an audio file in FolderB. Select the Save Media File As command to save the edited file. FolderA is presented as the suggested target folder. It really should be FolderB (the folder containing the original source file).