I tried your technique as well and it still didn't work.
This is the default floor mesh I load, and texture in the editor:
This is the punch, and this is where I put the punch. I select the floor mesh, and press I, as the manual says. I delete the punch afterwards and save the segment...but it does'nt save as a punched floor. I tried saving both times with and without the "no CSG" text next to the segments name.
This is what both techniques look like in FPS creator...
There's something wrong here, I'm hoping someone can help me.