This is something I had been plagued with for some time. My CAD package is pants at merging shapes and then a new feature in version 3 of S3D ( the Separate Connected Surfaces
function) has saved the day.
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
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!