It seems that you're using SR3. This is a known issue of that version. See this: http://community.qlik.com/forums/t/26246.aspx?PageIndex=2. SR4 works better, but it still has some issues.
[UPDATE] the workaround that I used before SR4 was: delete a folder from de QMC, restart the all the services, add the folder again.
I'm having a similar problem with QVS 9 SR3 (Small Bus. Ed ... without Publisher).
Since I always used QV reload through batch command, I'd like to know if your problem happened suddenly
or it was just the first time you tried to use QVS 9 reload capabilities.
As far as I saw this feature seems to be rather unstable.
Could you confirm that SR5 has solved this problem?
If so I'll try to do the same.
Thanks and regards.