Here's a simple model made up of two intersecting cubes: And here's how it slices....with an air gap where the two cubes intersect: And here's what it looks like after clicking the Separate Connected Surfaces function: Its best to use this function whenever you suspect your model may have intersecting meshes.
I remember having exactly the same issue with ReplicatorG....and I cured it by repairing the model with the online Netfabb service. But I don't have to do that now!