But like I said I waited for about 5 minutes real time with no visible maladies and I was still having the problems. I eventually prayed, got no response, but when I tried again about a minute after that I was alright.

If this helps at all. I was previously scourged for about 8 hours and then Vorondel called altruism on me. So if he took the affect of the scourge perhaps the coding of the creaking bones was still there.