I'm assuming the run command box in Configuration/Preferences Mail handling/Receiving is supposed to run Windows shell commands. No matter what I type in there, nothing executes when a new mail arrives. The same goes for the command box in the notifications plugin preferences dialogue.
This works for me in 3.13.2, e.g. I choose to run "notepad.exe" after manual receive, and I get an empty notepad window when I manually check mail.