Question about Fades and Flickering between HS/RL and Emus

[NewYears1978]

This might be an easy fix but what happens is this:

 

I am in HyperSpin and I click start on a game, and before the emu loads up the screen goes black for a split second, then shows HS again, then goes into the emulator.

Upon exiting the emulator the same thing happens.

 

I thought Fades would solve so I added in and out fades and now this happens (same thing):

 

I click start on game, Fade loads, then HS shows for a split second before emu shows.

Quitting emu, I see HS menu for a split second before fade shows then HS shows again.

 

Any way to smooth this out? I have seen videos (Simply Austins for instance) without this issue.  I thought it was xpadder profiles loading but I disabled xpadder and it still did it. I also messed with hide frontend, hide emulator, restore etc options but that didn't help.

 

Thanks in advance.

 

Edit:

A friend just led me to the fact that it might be from when the cmd window in retroarch pops up. I tried mame and the transition was smooth so he may be right..so is there any way to fix?