The animation flickers because different frames were captured through different filters. (The order is: panchromatic, red, panchromatic, blue, panchromatic, green, panchromatic, infrared, panchromatic.)
The images were taken on October 14, 2010, on Mars Express' 8676th orbit, and show an area within Noachis Terra to the west of Hellas basin, around 45 degrees south, 38 east. The other component has to do with the different look angles of the different channels of HRSC and the significant thickness of the cloud layer. In the first frame, HRSC was looking forward (northward) along its south-to-north orbital path; in the last frame, it was looking backward (southward). Because of this changing perspective, the upper-level clouds appear to move southward with respect to the lower-level clouds.