Try this GIMP plugin for performing a routine on multiple images simultaneously: "Batch Image Manipulation Plugin" http://registry.gimp.org/node/26259
Download and extract the package, open a terminal inside the resulting folder, and run:
make && make install
Then start Gimp, go to File - Batch Image Manipulation, in order to start the plugin. There you can add the multiple images.
As the question asks for inverting colors, add the corresponding manipulation set: Add - Other GIMP procedure, search for 'invert' and you will find 'gimp-invert'
OK, and before 'Apply' you can set the output folder which by default is
Hope that helps. Have fun GIMPing!