So today I decided to upgrade to the current beta of Ubuntu 10.10, codenamed ‘Maverick Meerkat’. After an hour or two of package downloads and installs, I was up and running with no major problems; save for one. I noticed that when I opened Nautilus, my default file browser, it did not appear to be using my GTK theme settings, instead looking like it was using stock styling and controls. After a bit of googling I found the (very simple) solution:

Remove or rename the ~/.gconf/apps/nautilus folder. Then, kill the nautilus process (pkill nautilus worked for me). After that, opening a file browser displays my proper theme as expected.