The discrepancies here are actually something I very commonly encounter with my students. Generally, such a gap between GMAC Quant scores and
Manhattan Prep scores can be attributable to discrepancies between your skill set and the skill set that the exam you're taking rewards.
Manhattan Prep exams generally reward mathematically-intensive, algebraic solutions, so if you have any gaps there, they'll be magnified on those exams and will subsequently lead to a lower score. On the other hand, GMAC questions are designed to test your reasoning skills and are crafted in a much more deliberate and nuanced way to ensure that they are indeed measuring what they intend to measure. The major consequence of this fact is that you can often strategically reason through questions on official GMAC questions in a way that you can't on Manhattan exams. Ultimately, your goal is to master the GMAT, not
Manhattan Prep's curriculum, so you should be comforted by your Quant performance on the GMAC exams: these scores better represent your skillset and should be more in line with what you score on the real thing. That said, identifying potential conceptual gaps based off of your
Manhattan Prep performance would probably be worthwhile, just make sure that you don't get so lost in the weeds on concepts that you forget to look at the big picture.