Yes. The problem is that there is a single build for the Video iPod for both 32 MB and 64 MB memory. The memory is initially set to 64 MB. This causes the overlay header to ask for it to be loaded into non-existent memory on iPods with 32 MB. Take a look at apps/plugins/sdl/wolf3d.refmap created when building.
I was able to get Wolf 3D to run by first building normally, then editing Makefile, changing to MEMORYSIZE=32, and rebuilding wolf3d.ovl. Then copying apps/plugins/sdl/wolf3d.ovl to /.rockbox/rocks/games/wolf3d.ovl on the iPod made Wolf 3D run.
Edit: The procedure to do this after a build is complete, in the build directory:
sed -i s/MEMORYSIZE=64/MEMORYSIZE=32/ Makefile
rm apps/plugins/overlay_ref.link
make
Verify the result via:
grep PLUGIN_RAM apps/plugins/sdl/*.refmap
You should see:
PLUGIN_RAM 0x0000000000000000 0x0000000001e80000
and not:
PLUGIN_RAM 0x0000000000000000 0x0000000003e80000
Wolf3D, Duke3D and Quake all worked for me, though I had a data abort when exiting Quake.