I'm a new user to xda-developers and I realize this is not the best place to post this, but it's all I can do for now, so hopefully I won't get flamed too bad. Another user reported this problem but did not know what to do so I thought I would post this in hopes he and the developer see this.
For some reason, nandroid does not backup /data/system, even when backing up "all", or just "data". I started using it and was playing with different releases and so forth, and every time I restored from nandroid I would have to extract data.tar manually, fix the permissions one by one, and copy the data back over after the restore, which took forever. This time I finally decided to look into the problem in more depth and realized the data.tar does not contain the system directory, which of course has all the UIDs and so forth for all the apps stored in the XML files.
With that said, Open Recovery is awesome! I love being able to have a full console and everything right there!! I'm using 2.09 and this has happened on multiple Photon Qs.