ive had landmarks be in different coordinates, different distance from the changelevel, etc. pretty much i did the opposite of what was suggested above
But the only thing that has messed me up, was compiling/running one map, and then do the same to the other, dont do that, compile (dont run) both maps then try it with the console.
in my opinion changelevels are illogical at times, but not all that hard to set up
But also do what muzzleflash and urbanebula are saying, itll prevent you from having random screwups.