I guess I figured out the reason (not the solution though). The splash screen does not work if the windows console is activated in the compiled program. I am not sure why is this!
Splash Screen not working, compiled using 2014b
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I created a compiled application using Matlab 2014b. I found out that since MATLAB 2014a, the compiler includes a splash screen by itself which appears while the MCR is unpacking. This was a solution to my previous problem of slow loading Matlab application.
I found on the Matlab Answers that some how this feature does not appear when the MCR is itself packed in the application, so I created a web download version but I got no success. What should I do? (My application includes a windows command window as well)