@Deerock69I don't think it was fixed. I'd advise to avoid saving in the puzzle rooms, especially the PEC room. Just put your 3DS into sleep mode and carry on the puzzle later.
Anyone going into VLR, absolutely play 999 first, or you will miss out on a lot of interesting developments. That being said, the two games actually have some big differences between them, in presentation and mood/atmosphere. VLR is more complex, much longer, more polished experience, but 999 is a more haunting, atmospheric and mind-blowing. Play 'em both, if you know what's good for you.