I don't know if it will help at all, but I thought I would post the script in case it might offer the developers some insight into what might be happening. It follows:
If $CMDLINE < 1 Then
MsgBox(0," Missing Parameter","Missing Media File Name Parameter")
$MediaFileName = $CMDLINE
RunWait(@ComSpec & " /c pushd ..","",@SW_HIDE)
WinSetState("Windows Media Center","",@SW_DISABLE)
ShellExecuteWait("C:\Program Files\MPC-HC\mpc-hc64.exe", """"&$MediaFileName&"""", "C:\Program Files\MPC-HC", "open", @SW_Maximize)
RunWait(@ComSpec & " /c popd","",@SW_HIDE)
WinActivate("Windows Media Center")
It's a weird little thing, and it seems to be the minimum of what I can make work consistently. It saves the current directory, actually disables Windows Media Center, calls MPC-HC, waits for MPC-HC to terminate, restores the directory, activates WMC, and then sends a WMC green button command followed by an extra enter, I found that the green button command would return me to the WMC menu pointing at my emby entry, and the extra enter command takes me back exactly where I should be in in emby (at the movie play screen).
It certainly wasn't an intuitive fix, but trial and error sometimes pays off.