With recent SVN builds, I've noticed the bevel modifier is causing mesh corruption when using the "angle" mode: some faces disappear when the modifier is used.
The faces are missing in both 3D View and rendering.
See test scene in attachment.
I'm running a home-built Blender on Linux Mint 13 32-bit.
Latest svn version: r52804
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This bug may be similar to 33425 "Bevel tool causing artifacts", but I'm not sure as in my case it concerns the modifier and not the bevel tool, and I think both used separate code to do the beveling.
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Indeed, the bevel modifier code is still completely separate from the bevel tool code, so this bug is not related to 33425. Though it may in fact end up being the same root cause that I am suspecting now: if all the api flags are not cleared by some operation, then a subsequent bmesh copy (used for undo/redo) may drop some faces.
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the issue is caused by my own commit r52588.
The cause of the issue is that ngon filling no longer does a remove-doubles pass.
We could have a doubles check still, though Id rather bevel modifier not make duplicate geometry.