Stupid question - do you have a valid license for Publisher? i.e. it's installed correctly and not timed out?
What does you Status tab look like in QEMC? Does it show all services as running with a green arrow, especially the "QDS" service?
In QMC, does it actually show any source documents? These would be located in C:\Documents and Settings\All Users\Application Data\QlikTech\Publisher\Sourcedocuments for Windows 2003, and C:\ProgramData\... for Windows 2008.
There are a couple of new service releases after yours, but I don't think that should affect such a basic feature.