Most modern CPUs support hyperthreading and report multiple logical cores for each physical core. Some programs run faster when scheduling threads or processes to use these hyperthreaded cores, while most HPC codes run more slowly. Rather than show all of the sparklines at half-height simply because the hyperthreaded cores are (wisely) not being used, MAP tries to detect this situation and will rescale its expectations to the number of physical cores used by your program.
If this heuristic goes wrong for any reason you will see large portions of unusual colors in your sparklines and the application activity chart (for example, bright red). When that happens, open this dialog and increase the cores per process setting.
You can find this dialog via the View → Processes and Cores menu or by clicking on the X cores (Y per process) hyperlinked text in the application details section above the metric graphs.