Hi Linda:
I don't have a line of direct sight into Disney World's pricing algorithm, but in general, prices tend to be lower when schools are in session, when crowds tend to be lighter. Here's my best guess: I'm not sure what days you are pricing in January, but Martin Luther King Jr. Holiday falls in January, and crowds tend to increase during days surrounding the Holiday.
Walt Disney World Marathon Weekend also falls in January, bringing in thousands of runners, friends and family. There tend to be fewer school holidays and special events through most of September (plus it's still hurricane season), so that's why I'm guessing September may be a less expensive time to travel to Walt Disney World.
There are a number of different opinions on when is the best month to visit Walt Disney World. In my opinion, October is the perfect month to visit. Schools are in session, so crowds tend to be slightly lower. Weather in October generally hovers in the mid-to-high 70's, and hurricane season, which starts in the summer, tends to taper off by October. Keep in mind that while the weather can get crisp in late October, it's usually not too cold, and Disney resort and waterpark pools are heated all year long. You can also take advantage of
Epcot's International Food and Wine Festival (World Showcase is transformed and features over 25 food and wine kiosks serving small plates of international food) and Mickey's Not So Scary Halloween Party.
As for best Resort, I'm not sure of your budget and interests, but I would look at the three monorail Resorts, starting with the Grand Floridian, then the Polynesian, and then the Contemporary. Animal Kingdom Lodge would be another great option.