Certain fields are encoded by Links when a record is stored. If links comes across two "|" characters in a row in those encoded fields, it will store them as "~~". When they are used, they are decoded back to two "|" characters.
Thanks Guys. It did not happen before. All of a sudden when I added a couple of new links (I am still developing my templates and adding all the mods) I suddenly noticed this. I was wondering if it was something that modified, that caused this.