As dwanthy says some actual title/author/isbn values will allow me to try to replicate your scenario and figure out what is going on.
The only other possibility I can think of is some sort of interaction going on in the "voodoo" that takes place in Calibre of merging results from the metadata download plugins. Maybe without the Goodreads plugin the tags being returned from the other plugins are being discarded, whereas with the Goodreads one enabled they are being merged. It sounds a bit funky but it is all I can think of from the steps you have described.
What dwanthy suggested above will test for that, or even more simply just disable all the other metadata download plugins except the Goodreads one. If you still get those tags with only the Goodreads plugin enabled then clearly I am completely and utterly wrong about it not being my plugin returning the tags.
