We believe they are from Windows Update. We have noticed this on multiple Windows 7 and Windows Server 2008 machines. After searching through the web, I came accross a forum where a user had contacted Microsoft for this similar issue and MS had to fix # of registry entries after running OneCare but that was just a temporary fix. The forum also mentioned it was related to an unfinished/horked-up update.

Do you remember the name of the folders? Are they only present when you run Windows Update? They may be also generated by third party programs. You may remember the names and search from Bing for more information.Arthur Xie - MSFT

Here's a list of some of the folders that are temporarily stored on C: drive. On this particular machine, there were over 60 folders and they are all EMPTY: 0a108efeb3cfd84c75b08a - 4/30/2010 1:48 PM 0ecf9af4e2ccccaa7503b3b52603ef - 5/1/2010 1:40 PM 1ac330260d504263497e93 - 4/22/2010 1:41 PM 1F269D71AFB29963422864B383534552 - 3/20/2010 1:41 PM 3e1043a7baf99ac94ed8d5f8a5451d - 4/28/2010 1:43 PM

The Windows Update downloads all contents to the folder %windir%\SoftwareDistribution\Download. If you're downloading from the Microsoft Download Center, IE may be write the temporary file into the cache before copying to the final destination. Windows Installer will create a temporary folder on the drive which has the most free space. After installing the folder will be deleted. Arthur Xie - MSFT

I understand exactly what you mean. Thats exactly the problem though, after installing the update, it DOES NOT delete the temporary folder.