Just to update anyone who's interested...
I've discovered that berries disappearing is actually a normal part of the game. I did an experiment on a freshly opened Emerald game; I planted two berries, and kept a close eye on them. One I would pick each time I got to it in time (as a control, as we say in the science geek world), and the other I left alone, didn't even touch. It took approximately 5 days for the untouched berry to vanish. So I don't know why it happens, but it's normal (annoying as it may be). I've also noticed some berries NEVER vanish, like Leppas. I've yet to see a Leppa Plant just up and say bye bye. It's also possible that others berries take longer to vanish, I chose the Pinap berry to test it on, because it's one of the fasted growing berries out there. Maybe one week I'll do a test on EVERY single berry possible, and write my own guide. I'll call it...the "Brownian Berry Glitch", Brown, of course, being my last name. ;-)
Although it's not really a glitch... it just sounds cool.
But the lesson is: DO NOT PLANT BERRIES UNLESS YOU PLAN TO PICK THEM.
This is especially important for those rare berries. Plant them, pay close attention, water, and pick. Do not plant another one unless you intend to repeat the process, as they usually do not last forever, like that little chick in the Pretty Petal Shop tells you. She's a liar!! haha