@Retro808 and I have done some testing here. Retroarch is apparently wonky in that it has some default bindings set for hotkeys that do some weird things, and the only way to fix it is to re-set those hotkeys. Basically, Retroarch's hotkey menu is lying in that there are controller hotkeys defined by default that don't show up in the menu (at least that's my best understanding of what's going on).
What has fixed it for @Retro808 is binding the same buttons to the same functions in Retroarch. So, for volume up and volume down, bind the same two buttons to that in Retroarch and in Big Box, and in theory that should fix it. Ultimately, though, this appears to be a bug in Retroarch.