So I've ALMOST gotten all the lightmap issues dealt with in my level. Truly, the lightmapping is the most frustrating thing I've encountered since the day my testicles got tied in a knot.
However, I still have one major issue.
Some models look absolutely terrible with lightmaps activated.
It could also be the lightmapper acting funny. We've found some bugs with the python script already that will be fixed in the next release, but we're going to be looking at it in more detail in coming days (by "we" I mean "someone other than me," though, so I can't give details