OpenGL clipping bug

[elfion]

Target OS: Windows 7 x64
Python2.7.3 x64
Numpy, PyQt, some small libraries taken here: http://www.lfd.uci.edu/~gohlke/pythonlibs/

The bug is described as follows: "When I click over a part or assembly, background goes white and model is clipped by half (!) (everything that's further from viewpoint than some plane is just plain white)". It's also strange that this bug manifests itself only with half of parts.
These parts are rendered strangely from the beginning: looks like first atom of each subpart is rendered at origin (0,0,0).
Bug behaviour is reverted if I select and deselect Crystal tool. (Maybe some crucial OpenGL reinitialization).