We know that time works differently in Pleasantville, as it only took an hour for the story to unfold in "real life". At the end of the film, when David returns, we hear the TV announcer say "And that concludes the first hour of our Pleasantville marathon".
In the DVD commentary the director, Gary Ross, explains that a Pleasantville episode lasts for 30 minutes, but that each episode's storyline takes place over about a week. So if Jennifer spends three years in college, it will only equate to a long weekend in our time. Given that Jennifer was both popular and self-absorbed at the start of the film, it may not be out of character for her to disappear for a weekend.