Ricky, I've installed GTK and setup for HalfLife, although from what I can see from the editing facilities, creating brushes like hollowed out cubes etc, appear to be ungrouped already. Although I'm unfamiliar with the build tools. I would suggest trying out Hammer or at least use the Zoner BSP build tools to see if this helps. Also, and this may help me to find the problem, if you send me the GTK radiant map file.
The other thing is that GTK Radiant saves it's files in .MAP file format which makes me think that the grouping tree isn't stored in this format, hence that's probably why GTK doesn't have a group, ungroup brush option. Hammer generates .MAP files but it's internal format is stored in a different file. Keeping grouping and other settings intact.
One thing I can also suggest which may help or not, but download my BSP test application, also found in the tools section of my site. This comes with an example BSP and WAD texture file. Try this application with your BSP and WAD file to see if the problem is still there.
Paul.

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