If you’re sure you’re not using CCD right now, then it just must be a nuance in your ODE build. And I think I know what it’s triggered by.
It would also explain why 1.0.1 works, while 1.2.x doesn’t. You see, in 1.2.0 a way to change the size of the capsule was introduced. This made it possible to bring the whole map to the right scale (hence the name of the blend file shipped – map_correct_scale.egg).
This, in turn, made everything much smaller. To find out how much, you can compare the blend files. You could even import, for instance, the tunnel object from 1.0.1 into map_correct_scale. It’s almost as big as the whole scene for 1.2.1 
.
I’m guessing that object of this new, small, size may not be handled properly unless some option is enabled.
The good news is that you can still use 1.2.x. The only thing you need to do is either find what that option is (if you ask on this forum, someone should know. Rdb most probably will, because he builds Panda) and rebuild ODE or… make everything bigger. You would, however, need to re-size the map in Blender and reexport the result into Egg. I’m not sure if the map from 1.0.1 would work with 1.2.x, so copying the map egg file might not be an option, but you could try. You would also need to copy the geom and body sizes from 1.0.1.
That way it should work, but obviously getting the build to support small stuff is the better way to go.
In fact, I now recall that I had a similar problem when I was working on 1.2.0 on the Panda build, and then it was fixed with some new ODE configuration option. Or it’s just my memory playing with me…