I just upgraded to 13.04 from 12.10 in a 64-bit Parallels VM, and the semi-transparent terminal windows I configured for Gnome Terminal are now totally opaque.
I'm setting transparency via Edit -> Profile Preferences -> Background -> Transparent background. This is also illustrated in http://www.ubuntugeek.com/howto-create-a-transparent-terminal-in-ubuntu-desktop.html. Adjusting the slider has no effect.
Any workarounds?
I don't know the root cause or a true fix, but I had the same problem after upgrading to 13.04 (not in Parallels, though), and on a hunch I ran xcompmgr, which fixed it. If that works for you, maybe that'll be a clue for someone better able to tackle this.
Previously I only needed xcompmgr if I wanted special effects or window manager-driven transparency, but maybe recent versions of gnome-terminal switched to compositing-based transparency rather than whatever method it was using before?