Sounds like an exception is occurring during the build. When you successfully build a repackager project, what usually comes next is 'Writing unmapped registry information to the Registry table'. So, perhaps what's happening is related to captured registry data.
Here's what I'd try:
Start by excluding all registry data to verify that this is where the problem is. This (I think) will make it build successfully.
Next, try disabling the registry related mapping options in the Advanced Settings of the project.
Lastly, if all else fails, just start excluding things until you find a particular file or registry key that is causing the issue. I usually do this in halves--exclude half the files, check to see if it works, if so, do the same for that subset, etc.