Yeah, the way it stores the codes is janky but it works. The INI reader will ignore the second line. It just reads everything between “next = ” and [CR][LF]. Very few people use this feature though, so fixing what is essentially a visual blemish is a low priority.
Setting the clock is a one-time thing, so you shouldn’t have to worry about that once it’s done. It’s also worth noting that when setting clock you do have to hold down MENU (not tap it) to advance the numbers. Then you tap NEXT quickly to set the hour or save the time. I know it’s fiddly but, again, it’s a one-time thing.
That still doesn’t explain any occasional glitchiness in the menus — are you still experiencing that? If so, you should be able to reproduce some anomalies in the “crash” test stream. If you can do that, I might be able to provide a software fix like you said.