MaryAlana, no it doesn't matter. Junction box up or down makes no difference to the panel. We've been installing them either way for years (depending on what makes wiring easier). So have all other PV installers I know. I am not aware of a higher failure rate, up or down, over time.
As long as they are mounted at a reasonable tilt angle the odds of water getting into the junction box are slim to none, the wires actually have a seal pressed around them where they enter the box. Even if any did, it'll dry out in short order (junction boxes are vented, and they get hot when sunlight hits the panel!).
One thing to keep in mind though, semi-related, is that if you're storing panels flat on the ground (outside) they should have the shiny (glass) side up. As mentioned, those junction boxes are vented and when stacked with the tedlar (white) side up it will fill up with water. This won't really hurt the panel, the cells/glass/etc is sealed in EVA and nothing can get at that, but it will make transformerless inverters throw a ground fault until the junction box dries out again.
-RoB-