On the topic of the Berry Glitch, Emerald is unaffected. At least, that's what Nintendo claims.
My Emerald game (official US version cart) has been frozen on the same day for years now. I think the clock in my room still moves forwards, but I can't do any daily events, and berries don't grow. I don't get a 'battery has run dry' message when I start it up, so it's most likely nothing to do with that.
Could this be caused by a similar problem to the R/S berry glitch? If a fix is found for R/S hacks, would it be possible to use that to find out what happens in Emerald, and possibly fix it?
EDIT: By the way, I believe the 'berry program was updated' message is from the FR/LG/E game. To apply the fix, you hold Start+Select on the GBA with R/S in; this causes it not to boot the R/S game and allows FR/LG/E to transfer the fix. Is the 'berry program updated' message in the R/S font, or the FR/LG font?
EDIT2: Disregard that, you were talking about Box :P
Even then, I'm pretty sure you get one of the Box emulator's pop-up messages rather than an in-game message window.