MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I've noticed since then that it doesn't connect regardless. I've never realized this because it wasn't a problem during printing. Try to use a brim instead of a raft and give it a shot to see what happens. In reality, at .20 res, that layer just gets deposited on top of the brim and that gap shouldn't be an issue. I remember it took me 1 or 2 tries until it was perfect but that's affordable I guess.