Perhaps I wasn't very clear. What happens is I enter an area like, say, the Energy Temple. After the area loads, Naija just floats there. I press a direction, and she'll orient herself in that direction, but won't move. She just stays in place. I need to use speed boost to get her moving, and about 50% of the time there's no further issue in that area. Otherwise, as soon as I stop moving, she'll stick in place again.
I went back through some save files, and I noticed that I first encountered this problem in the boss area for the Sun Temple. In fact, I found that if in the right position, Naija will hang in mid-air after the water level drops below her! Then there's no moving her until the water comes back up. She'd also freeze in that area if I jumped above the water, causing her to once again hang in mid-air, this time with no way of getting her down save for reloading the save file.
Before the Sun Temple boss, everything was coming up roses. Afterwards, I'd have this odd sticking issue in particular places in the game. It's fairly frustrating in its regularity. I'm starting a new game today, and I'll see if the glitch comes up again at the Sun Temple.
EDIT: In a new game with a fresh install, I encounter the same problem when I first enter Naija's home.
