I use MoI with a Makerbot Rep 2 and don't have any issues with meshing - actually I would say that MoI is one of the best pieces of software that I know for meshing/creating watertight 3D files.

I usually go from .obj over to Makerware for my export, and I only export solids.

I use the following (incidentally I learned them from another thread regarding exporting models for 3D sculpting) export settings:

output: "Quads and Triangles"
"weld vertices along edges" checked to "on" (although sometimes I forget and it seems to work fine)
"All" selected next to "divide larger than"
"set divide larger than" and "avoid smaller than" to the same value (I usually use between 0.5 and 1.0)

Happy printing!
-FDP

Update: I might have misunderstood your issue, it's getting late here!