I'm not that great with Coppermine and all those files, but I searched for "menu gone" and similar things and didn't see anything that looked like my problem.
I did the upgrade yesterday and it was fine. Now I did the patch today and was in a hurry so I ended up downloading the whole thing and upgrading like yesterday. Then I saw I only had to do one file. Anyway, now my menu is missing. My custom link is there, but the menu isn't and neither are the little "_ views" thing below the images. I'm not sure what I messed up in order to fix it.
http://colinhanks.starszz.com/gallery/
Got it!
I had more time to search and found the solution (the lang/english.php file was there but 0 bytes).
Solution was in this thread: http://forum.coppermine-gallery.net/index.php/topic,48047.0.html
Sorry about that!