multipart shape file polygon to supermesh

I am having problems importing polygons for use in creating a supermesh file.
This especially occurs for the scenario where I have carved out a hole (i.e. island) in the polygon and replaced it with a a second polygon.
(Note: in carving out the hole, the main polygon is divided into two parts, one for the perimeter and one for the hole)
I have checked to be sure all vertices are alligned.  But I still get error messages like the ones shown below.

        Warning: Polygon #7 ring 2 dropped since overlapping with polygon #7!
        Warning: Polygon #10 dropped since overlapping with polygon #7!

Do you have any suggestions to improve the work-flow processes or on the availability of specific GIS tools to create internal polygons?

The vertices of a polygon are counted counter clock-wise. The orientation of the vertices which are shared by the inner and by the outer polygon are clockwise. This is not supported by FEFLOW. Instead, the vertices must be counter-clockwise. You need a GIS tool which allows you to change the order of the vertices.

Mr. Heermann,
I know this is an old question, but did this solution work for you?

I beleive I have come up with an alternative solution, but I am still working at meshing the polygons.  Seems to be taking a bit too long. However, I got around the dropped polygons by splitting the main polygon in half so that it “cups” the island polygon from both sides.

Regards