I was using a 64bit Ubuntu but decided to switch to 32bit. Now, my Eclipse does not display overlay scrollbars anymore, but instead uses the old scrollbars. So why are they disabled on Ubuntu 11.10 32bit?
Overlay scrollbars were blacklisted because a workaround for a number of other bugs was causing them to glitch in Eclipse. These bugs have since been resolved (as far as I can tell).
Although it would seem only on the 32-bit arch ; I've never noticed them being blacklisted on 64-bit.
Precise lists the newer Eclipse 3.7.1 release and includes removal of the GDK_NATIVE_WINDOWS variable, so hopefully they have also removed it from the blacklist.