Hmm. That's an interesting problem. Here's what I would do:
1. Using the Direct Editor, check which component is associated with this entry within the ProgID table and then delete the entry using the InstallShield Direct Editor.
2. Go the the component from above, expand and select the File entry. Right-click on the file and select 'Extract COM data for Key File.'
This should put the COM data in the right spot. However, if the component name is RegistryData_*, odds are good that you can simply delete the entry and skip the above steps. This would indicate that you're package is creating a COM entry for a file that you're not installing--in other words, junk that you picked up whilst repackaging.
Hope that helps,