For some things Trenchbroom 2 is gimmicky like that. I recommend trying an earlier version.
As a work around I wouldn't use Trenchbroom2 to compile the bsp, only save the map file, and use a batch file to compile it afterwords, which is almost as quick.
Example batch file:
@echo OFF
SET mapname=some_mapname
QBSP3.exe -threads 6 %mapname%
::QVIS3.exe -threads 6 -fast %mapname%
QVIS3.exe -threads 6 %mapname%
QRAD3.exe -threads 6 %mapname%
arghrad.exe -threads 6 -v %mapname%
..\..\r1q2.exe +set cheats 1 +set game weapons +map %mapname%
pause
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This way you can fine tune a certain step, ex just do the lights:
arghrad -nocolor -minlighta 5 -maxlighta 170 -radmin 10 -choplight 64 -gamedir C:\quake2\baseq2\ -moddir C:\quake2\baseq2 C:\quake2\baseq2\mapname.bsp
pause