@jaredv - welcome to MobileRead.
I haven't had any problems with it, and I just tried it right now and it was fine. And no the Amazon/Goodreads relationship hasn't directly affected this plugin - other than there are some goodreads ids that have disappeared for some books, and covers that were missing while they reloaded more.
Give some specific goodreads id examples, also post the contents of your log in a spoiler. Make double sure you do have the Goodreads plugin enabled of course
. In fact try just having the Goodreads plugin enabled to make sure all output is only related to that.