The lower GPA can also be due to failing a class and retaking the class for a higher grade. Many schools will drop failed classes entirely from a GPA if the student retakes the course and passes on the second attempt. The LSDAS will include grades for all completed courses without regard to the individual policy of the school. So if you fail a class and retake it for an A, the LSDAS will include both a failing grade and an 'A' in the GPA calculation. That probably causes the biggest changes in GPA.
Other possible reasons include adding in undergrad grades from other schools (as a previous poster mentioned) and even deflating grades of schools that are not on a standard scale. (LSDAS curves all grades to the same scale.)
I don't believe withdrawn classes necessarily bring the LSDAS gpa down. I withdrew from a class (my schedule was overloaded) but it did not affect my LSDAS gpa at all, even though the withdrawn class was clearly noted on my transcript.
I'm sure once in committee, most schools would look closely at the cause of such a sharp drop in GPA. If it's something minor, such as an AP class from high school in some irrelevant subject, they would use the higher GPA. Unfortunately, depending on the formula used, a person whose LSDAS gpa is very low may not make it to committee. A 3.45 is pretty competitive at many schools, a 2.69 will get auto-rejected at most schools even if the LSAT is fairly high.
The index formulas for most schools are published and the schools that use degree gpa vs. lsdas gpa are noted on the formula sheet. If a school lets the lsdas calculate the index for them, they may never notice that the degree GPA is much higher. If possible, this person should write an addendum explaining any wacky gpa calculation problems or moments of academic coma on her part.