Would you mind adding a picture of the case to solve? There are so many things that can be going on...
There are no special case for the "real" top of a print. Any part that is getting toward the surface gets the required top/bottom shell thickness.
Is the top of the bottom cube completely closed or is it hollow under the top cube? Its pretty hard to stop a layer in mid air if there is no support under it.
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nightwish 0
There is a thread for the top Layers, who for some are not "closed" or lines don't touch.. here:
http://umforum.ultimaker.com/index.php?/topic/5375-top-layers-not-touching-um2
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