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Extruded surfaces of subtractive brush disappearing

I’m having a weird issue where I’ll be creating hallways/rooms/etc through extruding surfaces on a subtractive brush from within a much bigger additive box. I’ll leave that subtractive brush alone, go and make some more additive/subtractive brushes elsewhere that don’t intersect with this original piece, come back and find that **some **of the extruded surfaces have stopped subtracting completely, or rather the resulting surfaces are not showing.

http://puu.sh/7X3xi.jpg
http://puu.sh/7X3yx.jpg

Any idea how to fix this? It’s driving me crazy and has stopped progress on 4 separate maps/occasions.

Figuring out more but still no fix.

Seems to be related to moving vertices. The old position of the vertices where they overlapped seem to fail at subtracting altogether, or not update or something. Building geometry does nothing to help.
http://puu.sh/7Xooj.jpg

For this subtractive brush, the two left rear vertices used to be in the position indicated now by the inexplicable gap. Both brushes are subtractive, but the brush on the right has become broken in that it creates a gap regardless of where the vertices are.

Here’s the 2nd subtractive brush next to it which doesn’t seem to help any.
http://puu.sh/7XorA.jpg

I’m assuming I’m going to get zero help on this considering I don’t see anyone else running into this issue. I’m assuming this is a bug, but I don’t know where I should report it other than here.

edit: Going to post in Answerhub.