The second one should be executed as well, but it may well be that the application you're starting doesn't get the focus when it is started by Hotkeys or that the focus is onlt set to the application after the keys are already sent.
This is a bug in Hotkeys and it has been fixed in Hotkeys 2000 (which contains also lots of nifty new features). Hotkeys 2000 is currently in beta (beta 2 will be released this week). If you're interested I can add your name to the distribution list.