Yep, everything is extracted as I've done before when I've used GoMule. The 'GoMule' folder from the zip is on my desktop, I tried moving it but it didn't seem to matter. I actually run it maximized but I tried making it smaller and it didn't seem to change anything, however if I change the dimensions it temporarily goes back to normal until I hover over a button again and and goes to that mess of layers over everything (technically it's still usable but I have to memorize where everything is.)Welcome back. I have not played with GoMule on the latest version of Java, but one thing to make sure is that you are extracting all the files form the zip not just extracting GoMule.jar by itself or running it from the zip. Also where do you have the GoMule folder? Also have you tried making the GoMule window bigger?
EDIT: FIXED! Turns out it was RivaTuner Statistics Server onscreen display that comes with MSI Afterburner causing some strange interference. I recently updated my Afterburner version and it didn't occur to me until now.