Open the file in Netfabb.
Click Repair.
1) Right click the main body of the item and pick "Select this Shell"
2) Right click again and pick "Remove all Selected Triangles"
What you be left with is all of the "orphan/foating" shells.
This gives you a good view of what is going wrong.
Note: you'll obviously want to discard this repair instead of keeping it.. this is just a method to show you what is going on.
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Once you have confirmed that the the floating items won't affect your main shell:
Click Repair.
1) Right click the main body of the item and pick "Select this Shell"
2) Right click again and pick "Extract Selected Triangles as Part"
3) Right click again, and pick "Export"