It sounds like a bug, please contact to support.
It would be more helpful it you can provide a full stacktrace. It sounds like you have some anomaly in your catalog data...
We had the same issue. It looks like the issue was a result of the order of <Guid> and <Languages> node under catalog xml. It should be first and second child of <Catalog> respectively. The reason this error occurs is because how Mediachase code reads the xml stream. The import process expects <Guid> value to be first child of catalog and if it does not find in first child it assigns a new Guid and fails to process the catalog file as it would try to add a new catalog instead of overriding it. Moving the node orders solved the issues for us.
When we call to Mediachase.Commerce.Catalog.ImportExport.Import method in order to import one catalog from an xml file , we are getting an Sql error regarding "Violation of Unique Key" but it shouldn't happen because we set the method param "overwrite" as true.
Any comment or direction will be appreciated.