None of the above.
I tried MBuilder, and it worked correctly. So I had a look at the .bat file MBuilder created. I believe the problems were caused by the internal bsp_* commands from the menu. It uses something like "-gamedir ../mohaa" which isn't correct. Just replaced the "../mohaa" with the basepath ("g:/action/mohaa") and it worked.
I added these two lines to my "default.qe4" file:
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"bsp_Compile (fast)" "! g:\action\mohaa\radiant\q3map -gamedir g:\action\mohaa $ && ! g:\action\mohaa\radiant\q3map -vis -fast -gamedir g:\action\mohaa $ && ! g:\action\mohaa\radiant\mohlight -fast -gamedir g:\action\mohaa $"
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"bsp_Compile (final)" "! g:\action\mohaa\radiant\q3map -gamedir g:\action\mohaa $ && ! g:\action\mohaa\radiant\q3map -vis -gamedir g:\action\mohaa $ && ! g:\action\mohaa\radiant\mohlight -extra -final -gamedir g:\action\mohaa $"
And that does the job. No more MBuilder needed.
If someone ever has a problem with his Radiant installation (no popup menu when pressing the right mouse button etc.) try deleting the MoHRadiant registry key to reset the configuration, then do all settings again. With all those shortcuts scattered around the keyboard, it's too easy to do something wrong.