Dear Rubio, I recently came across extacly the same problem. As far as I understood, Matlab pause() command have some stability and accuracy issues (many posts suggest using java threads instead), and surely cannot be compiled in standalone apps. So, what I did was to solve the problem not using pause but with a simpler and more stable msgbox, as below:
uiwait(msgbox('Press ok'));
Overall, the user must give a keyboard input in both the cases (pause and uiwait), but the second one...works!
I hope this solution may be suitable also for your case. If you find out any smarter one, please let me know!
Best Filippo