PCSX2 app question

Hello there.

Thanks for the amazing app!

Using the PCSX2 app, I have gone into the emu settings and set Align Sprites, so that the black lines/boxes are fixed, and when I load the emu directly, its fine and the setting is applied. But, when I launch through retrobat, it overrights the hardware hacks Align Sprites settings, so the black lines come back.

Any help would be great - many thanks.

K