Custom screen resolution does not load when launching a game

I made a 1080p 53.20hz screen resolution to use with Mortal Kombat games on FBneo. This works well with such games, the vertical scrolling scrolls smoothly.

The problem is that after saving the custom configuration it does not load correctly. I mean, it loads everything as configured (1080p, Full screen. No window mode, integer scale, etc.) except that instead of starting at 53.20hz it always starts at 75hz like on my desktop.

Is this a bug or is there something I’m doing wrong?