Thank you for posting the screenshot because it helped me to understand the issue that you are seeing.
The snapshot mode of Repackager is currently capturing two copies of each shortcut when repackaging on Windows Vista and newer. It is safe to delete the copy that is off of the WindowsVolume for each shortcut as a workaround.
We have an issue reported for this behavior with number IOA-000053428.
We have made enhancements to the Installation Monitoring capture mode for our next release, and it will not have this issue.