I was looking at my auction that Todd_Vinton won and He said he had paid. Out of habit, I always check my rupees balance before doing anything. I still had 18,000 rupees. Then, I wondered what was up and I hit the rupees tab. My balance changed to 50,000, which I had 2 days ago. It also said they my most recent transaction that brought me down to 50k was today, about an hour ago. I have not logged on today. My conclusion was that the server clock was 2 days behind. Also, I blurred out the location of my horse summons and my locked chests. >.>
Update: now I have received my payment and have about 32k, but when I hit rupees it is still out of wack.