I have phpVirtualBox set up such that it runs from a symlink directory in the VirtualBox user's home directory -- Apache is configured to run the code in the directory /home/vboxuser/phpVirtualBox, and that is a symlink to phpvirtualbox-4.2-4.
If I switch the symlink back to the 4.2-4 directory, it goes back to working exactly as before in my browser of choice.
Did you clear your browser's cache after upgrading?
Yeah, that was the first thing I tried, both browsers (IE & Chrome).
Hmm, a bunch of 403:Forbidden responses, looks like everything in /js and /rdpweb. Looks like when I unzipped it, all of the directories got permissions of rwx------. Odd that it wouldn't work, since the site is supposed to be running as the same user.
Fixed up the permissions and it works fine now.