Ahah! You are interpreting the daily short report incorrectly. Of course there is a temporary short on most every trade. How else could an MM make a market? Nearly 100% of those intra day shorts are covered with in a few seconds. Less than 1% take a full day to cover. However, the new rules require these trades to be reported as shorts, even though they are not short sales as you and I know them.
There was an excellent explanation of this process posted on another board by Dave Patch of investigatethesec fame. Later tonight, I'll see if I can't dig it out and post it here for everyone to see.