I just had to deal with the same thing while making a testing package for my new project. The Track Packager will try to add whatever folder the objects are stored in, and in this case it was a special project folder I made specifically for the track. Unchecking this folder from the list fixed the issue. This issue ought to be posted in the tools listing. It won't even let you add the files in manually.
Speaking of which, everybody should always put their object files into project folders (create a subdirectory under objects, a directory specifically for your project) to make manual uninstallation less of a pain in the ass. Before NL supported this, I always named my files so that they could be easily identified and deleted, by including a prefix of the project name's initials. (i.e. Every relevant texture/object file on Santa's Sleigh Ride starts with "SSR", e.g. "SSR Texture..."
Not sure on the subscript out of range nor runtime error 52. My guess is that some issues may occur with certain file names or characters, or both. That and it's always worth double checking for zlib.dll and the patch.
Edit: The track packager is pretty much outdated trash now. It won't include reflection maps for objects which I didn't even notice when I did Neon Nitehawk (oh well, too late), and it won't include chain lift sounds either.
Looks like I'll just pack up all the files the old fashioned way. I'd rather that than use some random .exe installer.