Video Editing: Length of clip differs based on blend type or bug?

Hi all.

Im using Blender for video editing and I’ve encountred something wierd.

I have a background clip looping. So far so good. When I on top of the looping clip add my .mov alpha channel lower third graphics, that lower third stays too many frames, before it outs. Well…why is this strange? If I delete the background loop video, the lower third animation suddenly stays for a shorter period of time (as it should). It seems that when a clip is on top of another one with alpha channel, the frame rate goes bananas.

Help is heavily appreciated!