Hey, so I'm having two problems with my GECK. One is that the heightmap editor crashes the GECK if I try to paint or generate terrain. Second problem is a strange view problem when I'm actually trying to edit stuff in my new world space, in that things turn invisible when they should be obscuring the terrain behind them, really irritating, only hair seems to stay visible. *shrug*
The z-ordering issue (Where things obscure items that should be in front of them) is a common graphical glitch for me. All I can suggest is hitting 'a' a couple times to toggle the lighting (and thus, reset the device state or whatnot). If that doesn't help (IIRC, this happened when I was dragging back and forth between my two monitors), try restarting the GECK. Worked for me.