Give this a try. In Publisher, under the Diagnostics heading, click on Logs. Enter a timeframe a few minutes before and a few minutes after the error you got and click search. If you see an error that says something about an Xml error where the root element is missing, there is a corrupt .xml file that is causing your problem. To find the file, navigate to C:\Documents and Settings\All Users\Application Data\QlikTech\Publisher\CommandCenter\Reporting\0adf0770-19f0-4efa-a25e-1001436162ad and look for a .xml file that has a size of 0kb. The easiest way to do this is to sort the list by size. If you find one with a 0 length, that's the corrupt file. Rename it by adding your initials or something like that to the front of the name. As strange as that sounds, that should take care of the problem. Qlikview spins through these log files when you fetch job histories and if there's a corrupt file out there it doesn't know how to handle it.
Hope that helps,