This article discusses the problem of time registration between navigation and imaging components on Micro Aerial Vehicles (MAVs). Accurate mapping with MAVs is gaining importance in applications such as corridor mapping, road and pipeline inspections or mapping of large areas with homogeneous surface structure, e.g. forests or agricultural fields. Therefore, accurate aerial control plays a major role in efficient reconstruction of the terrain and artifact-free ortophoto generation. A key prerequisite is correct time stamping of images in global time frame as the sensor exterior orientation changes rapidly and its determination by navigation sensors influence the mapping accuracy on the ground. A majority of MAVs is equipped with consumer-grade, non-metric cameras for which the precise time registration with navigation components is not trivial to realize and its performance not easy to assess. In this paper, we study the problematic of synchronization by implementing and evaluating spatio-temporal observation models of aerial control to estimate residual delay of the imaging sensor. Such modeling is possible through inclusion of additional velocity and angular rate observations into the adjustment. This moves the optimization problem from 3D to 4D. The benefit of this approach is verified on real mapping projects using a custom build MAV and an off-the-shelf camera.