I was having this exact same problem. After reading through one of the bug reports linked to above, and then following one of the links in there, I found this question: Geforce Go 7300/7400 blacklisted, can I still run Unity?
It turns out that the video card (in my case a nVidia 7300) was blacklisted, and even though I was logging into "Unity" and not "Unity 2D", it was still falling back to 2D mode because the card is blacklisted.
There is a workaround there about installing the nVidia 173 drivers and forcing Unity mode, and it works for me. I also tried it with the latest drivers, hoping the compatibility issues has been fixed, but the system locked up as soon as I logged in, so I had to go back to the nVidia 173 drivers.
The important parts from the link I posted:
/usr/lib/nux/unity_support_test -p. If you get a red "no" next to "Not blacklisted", then you've got this issue. Once you install the nVidia 173 driver, you can edit
/etc/environment and add the following line:
Log out and back in, and you should be set. You now have to re-apply the settings in CompizConfig, but this time they should be respected.