I just want to give our experience on this problem and say thanks to Pompon for the solution.
We have vCenter 5.5 installed on Server 2008 R2, both system and user %TEMP% & %TMP% points to a temp drive T:, databases are located on a remote database cluster and problems arose at first reboot.
The delayed start of "Vmware Secure Token Service","Vmware Identity Management service" and « Vmware VirtualCenter Server solved our problem! Our dependencies was correct by the way.