@kabammi If you don't mind being a tester, try out this update site: http://sites.imagej.net/ThreeDViewer/
There is a growing list of infamous problems with 3D Viewer, and the Java3D library that it is based on is not improving (and no improvements are planned). We spent the past couple of weeks working on a replacement called... ThreeDViewer, which is still very, very new and things are changing, but you can already load meshes and voxelize them (i.e. you can use ThreeDViewer to access imagej-ops functionality through viewer menus). The feature list is growing quite rapidly and will almost certainly grow beyond those of the existing 3D Viewer.
We're just really trying to move on from 3D Viewer instead of solve these problems for code that is now rapidly bitrotting.
It would be very much appreciated to get some tests on Windows as well, we've mostly been testing on OSX and Linux, but the code has been written such that it should work in Windows as well.