The silver glitch is probably something wrong with the game.My silver version has saved every time (i have 2 backups though, just in case). I doubt you'll be able to fix it so you might as well get a new one.They cost a couple of Ł/$ off of ebay.
I don't know about the ruby and sapphire, but this glitch doesn't seem to be a good thing.You need the tides to change to get into one of the caves in the north east of hoenm, and the berries are useful for contests.