Perhaps I should clarify- I did those patches ages ago, hence my referring to the "old Berry Glitch," as it's not a glitch that should be around any more. This is a copy of Ruby version that I've owned since 2003-2004 and it has done plenty of trading with FR/LG carts and with Colosseum on the same save that still exists. I even tried loading the patch program in my copy of FR and patching the game just in case I somehow managed to avoid getting the patch after all, and the Ruby cart comes up with an "Unable to update" message which I can't imagine is indicative of anything other than that it's already been updated.
The weird thing that's going on here, and the reason I gravitated towards the Research forum and started thinking about dumping my save (which I've done now, I'm just too inexperienced/stupid at hex-editing gba saves for the moment to actually do anything with the dumped save other than play it in VBA), is that I've somehow managed to replicate the effects of a glitch that should have been patched out of the game years ago. The obvious answer to "how" is that I'm experiencing continuing effects of the battery running dry despite putting in a new battery because the game doesn't know how to restart particular features after they've broken due to the battery (not due to the aforementioned glitch that Nintendo patched out themselves) and I want to research exactly what happened. There's one person in the Gen III Q&A thread who's mentioned experiencing the same issue under the exact same circumstances but overall it's not something that's been documented because the rare folks who actually change the dry lithium cells in their RSE carts mostly seem to just start new games once they do so.
What I want to do with the save file I've dumped is unpackage it and take a look at what's going on with the Loamy Soil data using a hex editor and see if there's anything insane going on with the minutes remaining variables for my berry bushes or if there's anything else amiss. Right now I lack the means to unpackage it though there's plenty of useful reference information on Ruby/Sapphire save file data structure on furlocks-forest (which I can't link yet since the board software won't let me until I've posted more).
Alternatively, there's the possibility I'm a complete idiot and it really is something simple I can patch using official Nintendo stuff and I just haven't done enough Google research. Somebody talk me down from my insane scheme if you think this is the case.