Same here after update
My Droid Razr M just updated a few days ago to Android 4.1.1 and now I am having the same problem with a twist. The images that were in that folder before the update are still hidden from the gallery... any new images that have b een placed in that folder since the update show up in the gallery. You can still click on the album and the picture, so they aren't "ghosts" as described above.
I'm not sure what the deal was with the update that caused this. The only other thing I can think to try is to recreate the .nomedia file so that it has a file creation date after the date of the upgrade... may be something funky with file dates. Other than that I'm at a loss.