It looks like the Modify ePub plugin is working just fine.
The problem you are seeing in that output is that you have an old and incompatible plugin called "Goodreads Covers" installed (the predecessor to the "Goodreads" plugin which was a consolidation of two Goodreads metadata plugins that occurred when calibre 0.8 was released).
You need to get rid of that old plugin. Run this from a command line prompt:
calibre-customize -r "Goodreads Covers"