I have just tried to repackage a large piece of software and repackager (with default options) has not captured any of the registry keys. I know that there are plenty of them. My .nir file does not contain them either.
I would like to suggest you to check if the registry check is included.
By the way, make sure that the repackager is running on the same machine where the to-be-repackaked application is installed if you want to capture the registry changes.
This issue has been identified and will be fixed in our incoming MP release.
For now, the work-around is: Never disable your WelcomePage . If you have checked "Don't show next time" on welcome page, you must remove the isrepackager.ini file from Windows folder, or modify the "ShowWelcomePage" line to "ShowWelcomePage=1 " in the file.