Ok cool.
I have some more information though (and a bug report/feature request):
I copied my solution to another location to try and isolate the problem. Interestingly, everything immediately looked fine: all code that is covered is also indicated as covered. (Well, I didn't check everything, just the problem spots.)
I also noticed that none of the files I excluded from metrics coverage are excluded. Apparently you're saving the full path for excluded files? That should really be changed to relative paths.
Anyway, since getting rid of the exclusions I think maybe they have something to do with it.
On the other hand, deleting the exclusions directly, at the original location, doesn't seem to solve the problem entirely. So, I dunno.