Okay, so.. here is some more info..
Seems like if I modify the tile's collision poly, then Chipmunk separates it into another group or something. Moving the points back won't revert it, I had to right click and set the collision poly to bounding box for it to combine properly.
Maybe there is a flag somewhere that is set if you set the poly to bounding box, and it is toggled when moving the points?
Anyways.. kind of interesting.. Basically if a tile is considered a polygon(not bounding box), then it won't combine with tiles that are considered of bounding box type.