As I stated before, I've been using NTFS, and some issues have shown up:
1. I mentioned that Wii Fit Plus would not load up correctly at random times-haven't seen this in action personally. This is according to the wife.
2. Mario Kart Wii "delay freezes". What I mean is that while playing with the family, we'd starting picking stuff. When we get to choosing cars or any screens afterwards, randomly the graphics for the cars/drivers and each successive screen would not have the picture/movie files playing. Text and such would still be visible, so you could choose your car and course, but you wouldn't see any of those preview pictures/movies. And by randomly, I mean once it started, the pictures/movies were always gone on all the screens. Once you picked a course, it would freeze completely. You could go back and forth between all those selections, but you would not be able to back out to the main menu either. This has happened about 5 times in the 2 hours combined we played with it over 3 days.
3. However, in the times I've played Skyward Sword for hours on end, I've had zero problems. Haven't really checked other games.
I'm going to remove everything from the drive, and reformat to FAT32, and see if that helps. Before that, I'll try updating everything with the modmii as suggested (to save myself some research time). I'll be interested to see what's out of date. Shouldn't be too much.
I think I have read that NTFS may have some issues, while FAT32 has minimal, if any. Thus my reasoning that may be the culprit.