I recently investigated some things about .vmf files. I accidentally noticed that when modifying in Hammer some vertices, even if they appear to be in an exact position, the actual plane parameters are quite odd.
For instance, we have this 64x64x64 cube, positioned at 0,0,0 with its bottom-left corner. Here you can see the plane parameters of the top and bottom face: Now I'm going to rotate this on Y by 180 degrees: The plane parameters now look like this: What's happening here? I believe this doesn't affect how map compiles( although... the compiler interprets nothing else but this .vmf!). But if this happens on most of the brushes, and I use quite a lot CTRL+M, I can start to imagine why sometimes vrad simply stops compiling without reason(I have talked about the issue of vrad.exe stopping the compile on bigger maps( CPU 0%) several times).