Measurement nerd here with an (unfortunately) incomplete answer. The measurement theory behind the GMAT scoring algorithm has three parts... 1) how easy a question is to guess on 2) the difficulty of the question and 3. the amount of information the question gives the algorithm about the test taker.
Let's assume that the algorithm is working correctly. (If you really feel like it isn't working properly, I'd report it to GMAC- definitely something they'd appreciate knowing if it is in fact broken!) Now without seeing these values for the questions your student got right or wrong or knowing the specific GMAT scoring algorithm, it is literally impossible to know exactly why they got the scores they did. That said, if I had to guess, it's some combination of:
1. Some questions are just going to give the test more information about a test taker than other questions are and are therefore going to be valued more by the algorithm both when it's choosing questions and when it's scoring.
2. The difficulty of the questions you miss is as important as the number of questions you miss, if not more so.
3. For the quant section, percentiles tend to drop off precipitously. A Q49, for example, is only in the 74th percentile even though anyone would agree that it's a pretty darn good score.
That said, one of the important things to remember about the GMAT scoring algorithm is that you don't break the world record for the fastest marathon by knowing how electronic timing works - you do it by running really quickly.