If you're already rooted and currently on a custom ROM then yes you can wipe and flash another or even the same ROM or you can even do a ROM restore from settings. Obviously you will want to backup anything before you do anything but I would NOT make a nandroid backup at this point due to the issue you have. It will likely be found in your nandroid backup as well. I'd recommend a clean flash. Remember that ROMS that have some of the Note 3 features tend to have issues and that's why I personally prefer STS or the stock rooted MK4 ROMS from Slesh and LorJay's threads. No issues with either. Also you may want to flash a god compatible recovery such as Phil's recovery version 6.07.9. Since the Jellybean/MK$ upodate there has been compatibility issues with some custom recoveries so I thought you should look into that as well before flashing a new rom. Your issue seems to be unique.