Use SendKeys to Execute the Opening Command on the Putty window after logged in + NEWLINE. Tested and working.

mRemoteNG/Connection/Protocol/PuttyBase.cs

@@ -203,6 +203,10 @@ namespace mRemoteNG.Connection.Protocol
                                                     string.Format(Language.PanelHandle,
                                                                   InterfaceControl.Parent.Handle), true);
 
+                NativeMethods.SetForegroundWindow(PuttyHandle);
+                var finalCommand = InterfaceControl.Info.OpeningCommand.TrimEnd() + "\n";
+                SendKeys.SendWait(finalCommand);
+
                 Resize(this, new EventArgs());
                 base.Connect();
                 return true;