Have you been using -samples? Looks like you've been using an older post-SVN version of NetRadiant. The solution would be to update to the newest version which doesn't have the bug.
I have been using -samples, but I've also been compiling from source so it should be ....really recent. Although, Misantropia fixed a script that runs during compile (compiling netradiant) so...if he mirrored netradiant into his git repository and fixed that script, I'm compiling code that's just the latest version as of the date Misantropia mirrored the code. However, this was done less than a month ago. I've also been using -samples on the same computer just on a slightly different map (literally the same map, minus 16 brushes). Maybe my system just encountered a flipped bit due to cheap hardware or heat issues?