OK, that's a little surprising. Maybe try putting a "drawnow" after opening it?
You are right that nothing will be shown until the MCR has been loaded/initialized. The only way around that is to write a wrapper around your executable that shows the splashscreen before launching the MATLAB deployed app. Obviously that would have to be written in something other than MATLAB (which requires the MCR!).
12 Feb 2013
Show a splash-screen during MATLAB application start-up.
I am trying to use this for compiled programs and hope this will show up soon after the program icon is clicked. In general, it will take a while before anything can happen on the screen, probably because MCR has to be loaded. In my case, the program also goes to look for the paths of file I/O that are saved from the previous session. When I call this in the _OpeningFcn(), it did not show up until close to the end of waiting time. Wonder if there is a solution for it?