As a matter of curiosity, where all are Photo Beta prefs stored? I've dragged Affinity Photo Beta to the Trash. Gone to User/Library/Prefs and dragged "com.seriflabs.affinityphoto.beta.LSSharedFileList.plist" to the Trash and deleted both. But when I re-download the newest beta (yes, the previous download was also trashed) and install it, it comes up with my previous non-default preferences in place. Where is it getting them?
The reason it might matter is that if MountainLion has screwed up something in the prefs that is preventing Photo Beta from opening NEF files, then a new build is prolly not going to fix anything.