The times I've made dives so far, I've always had to be really careful when I'm descending. I don't know what the problem is, but for whatever reason I have to equalize extremely frequently all the way down. What I've found works best is to use a combination of equalizing techniques - usually I'll do some Valsalva, but Toynbee (swallowing while pinching nose) works very well also. The best thing for me, though, is simply to swallow normally while I go down, but just do so more frequently. It's sometimes hard to do, what with the air being drier than usual, but it works the best.
Unless the hood was pretty tight, I don't think that would have caused a big difference...I usually dive with a hood, and it's never caused equalizing problems for me before. Your ears should go back to normal pretty soon after the dive, but I've had mine popping and such for a day or so afterward sometimes, and it hasn't caused any problems.
Granted, I'm still a pretty new diver, so this is all mostly based on various things I've read and personal experience.