Personally, I've never had it happen on the Manage Perks screen, only the Leaderboards. However I asked the dev about it and he states that if the game freezes up on a player because they looked at the Leaderboard, and the game happens to be in the middle of saving, there's no telling how it could affect the game. It's a bummer, but the only open at that point would be to delete the save or not edit perks.
He's pretty ticked off that he can't do an update yet and that it'll take 4-5 weeks at least. But that it would be a good idea for people to back up their saves. Things should be fine as long as players don't check the Leaderboards in the middle of a save.
Out of my own curiosity, doesn't the game freeze up if you go to Manage Perks after choosing a song (on the Start/Difficulty/Visual Intensity Screen) or just when you go to it from the main menu?