This happens if you have an older Nookcolor purchased before v1.2 (when the app store opened). When you did a factory reset it set it back to an older version that didn't know where to put the apps. Even when you update to the newest version, those apps are already filed in the wrong place.
The only way to fix this is an erase/deregister. Hopefully you haven't set up too many preferences again so this can be as painless as possible.
On a brighter note, v1.4.x seems to replace the factory image as well, so you should not see this issue again in the future. I found this out with a recent factory reset and I was still at v1.4.2 I wouldn't recommend testing this though