Hi Chipp, yeah something at one point got confused by that little slivery surface there and things got joined together on opposite sides of it. Things shaped like small thin slivers like that can cause various problems.

I was able to repair the object by separating out the 3 faces in each of those places which was 2 fillets and then that little sliver between them and then doing an "untrim" operation on all of them to get rid of the current messed up trimming boundary and restore their full underlying surface. Then after the untrim the pieces joined together ok with the join command to make a proper solid, I've got that in the attached file which should now boolean properly for you.

Probably the actual problem is some kind of bug but it's a bug in handling some kind of thin slivery surface condition in filleting, but somewhere in your original curves there is probably a little tiny 0.005 length curve segment as part of the profiles used for construction and it would be better if something that tiny was not in there.

If you are curious about how to do the untrimming stuff, there is some more information on untrim here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=444.4

And there's more detailed information on this kind of low level surface repair process in the object repair tutorial here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=446.17

Hope this helps!

- Michael