I have seemed to have the same problem, I am deploying for a CC Team, and have noticed that this happens when Photoshop is installing.
I have created a SCCM package containing the Photoshop by itself and with other software, both of these packages stops the Explorer.exe without restarting it. Packages without Photoshop does not stop/restart explorer.exe and works as intended.
Mark have you tried creating a package only containing Photoshop to see if it have the same problem?