I'd like to apologize for this lackluster bug report, by the way. I was too tired when I wrote it. Sorry. I'll fix it a bit now.

I was using the most recent Windows test build at the time. I'm using Windows 10 Home Edition, 64-bit.

Just to give more information:

This issue occurs when you click on "OK". If you check, the checkmark will still be there while the Settings window is opened. It will also stay there if you click "Cancel" in the Settings window.

It's been a while, but I have more info on this.

When you select the "Native 59.7" option from the "FPS target" menu under "Audio/Video", the program writes "fpsTarget=59.727500915527344" to config.ini.

When you open the Settings window, it reads the above mentioned fpstarget setting and interprets it as 59.73. From there, when you select OK, the program writes "fpsTarget=59.73" to config.infi.

The two options thus write different results to config.ini. I don't know which would be correct in this instance. I guess the 59.73 is?

The correct value is approximately 59.727500569605832763727500569605832763..., or exactly 262144/4389.

Hey. I found another version of this bug.

In the drop-down menu, select 60 fps. Then select native from the same menu. Close the emulator. The following will be written to the ini:
fpsTarget=59.72750056960583

It will stay this way until you go to the Settings menu and select OK. Then this will be written to the ini:
fpsTarget=59.7275

Also, for some reason you can click on the checkbox in the drop-down menu again. It will deselect all options in the fps menu if you do that.

EDIT: Oh, and of course I'm using the most recent MGBA build at the time of this post. I always stay up to date. :3

Both of these should be fixed now, thanks.