Baked Lighting Issues

I'm trying to bake some lighting using the Progressive Lightmapper and it's working pretty well, but for some reason some areas of my scene are not being generated accurately.



The settings are pretty low to iterate quickly, but even with hundreds of direct samples and thousands of indirect samples and a higher res map I get the dark square areas and some areas just don't seem to cast shadows at all.

Any tips?

 

Here are my lightmap settings



And here is the produced lightmap.



The square areas of the lightmap are the problem.

Here's another image of the output:


I've tried a bunch of different settings and can't seem to get rid of the big dark blocks...