Evaluating the performance of reconfigurable computing applications in multi-tasking systems using simulation (as can be needed in early design-space exploration) faces several challenges. The complexity of full-system, cycle-accurate simulation prevents executing applications to completion. One must sample only a portion of execution; yet unless care is taken, the measured performance for the sampled interval will not be indicative of the complete execution. Although this is generally a problem for simulation-based evaluation, the problem is exacerbated for multi-tasking systems. This paper therefore presents work to develop a performance evaluation methodology that accurately measures hybrid (both hardware and software) application performance, accounts for additional overhead introduced by hybrid resource management (such as run-time allocation of reconfigurable hardware), and correctly compensates for momentary imbalances in processor time allocation that are only artifacts of the (necessarily) short simulated execution timespan and would balance out over time.