Grades and test scores aside, can a learning difference affect a student's chance of acceptance?
As with so many things in college admissions, it depends. Some schools don't even maintain wait-lists. Some take several students from the list, some take very few. This is also true of individual schools from one year to the next. A college might take 15 students from the wait-list this year, but next year only take three. Your best bet is not to stress about your chances of turning that wait-list status into admitted. Express your ongoing strong desire to attend the school via a letter, then put your wait-list worry aside and focus on choosing from among the colleges that have already offered you a spot.