I use Strata 3D CX 7. When different parts intersect the thickness goes under minimum. My knot lid, tall ochoko and expanding ochoko all have parts that are below the minimum thickness but they were printed fine.
What material are you printing in? Our checks are manual, so just because something got through our checks doesn't mean that it fully complies with the rules.
Check out my explanation here: https://www.shapeways.com/forum/index.php?t=msg&&th=7 825&goto=41969#msg_41969 One choice is to run the model thru https://cloud.netfabb.com to make sure it's a single shell.