I do not think I made the situation clear.
You are 100% correct, the winnings go into my running total. It shows up and all is fine - arena winnings went to 0 and my account went up...
...until I logged back in. My current amount reverted back to a what it was before I collected my arena winnings and the arena winnings went to 0. The net effect is that I lost all the arena winnings for that day.