I figured I would do a quick and dirty installer with a VS 2008 deployment project. I used the Registry Editor to create some keys, importing an exported set. There were keys that had no values. The vdproj built ok. The resulting installer installed without error. While trying to figure out why my application wasn't running, I checked the registry keys on the target machine with regedit. An error message was displayed for the keys without a value.
I checked everything in the Registry Editor and it all looked good.
Eventually I manually added (Default) values (as explained above) and rebuilt the vdproj. After that the keys installed and read ok. This corrected the application problem as well.