i've encountered the same problem as discussed here and found the problem in our configuration: UltraVNC 1.x
We've got 2 PC's where KES 10.2.2.10535 (mr1) and NetAgent 10.2.434 Patch C on a KSC 10.2.434 Patch C running von Win7 x64 Pro and Win8.1 x64 Pro, each installed and running UltraVNC 126.96.36.199 x64 without any problem.
Some other PC's on Win7 x64 Pro, KES 10.2.2.10535 (mr1), NetAgent 10.2.434 Patch C and also installed and running UltraVNC 188.8.131.52 x64 encounter a freeze of explorer.exe of about 1:40 minutes when opening the window "notification area icons".
Also i discoverd in the local logs of KES every 5 seconds two messages from program "Windows Explorer" that KES found not-a-virus WinVNC (seen on screenshot).
I tried both x86- and x64-version of UltraVNC - no difference.
When i uninstall UltraVNC, the freeze and the log entries are gone.
I tried deleting the registry key of the ContextMenuHandlers mentioned above - no difference.
With KES 10.2.1.23a and NetAgent 10.1.249c installed the freeze of explorer.exe doesn't appear.
I don't know, why 2 PC's don't encounter the problem, but these are Administrator-PC's with some different software installed.
I hope, this information helps.