I upgraded Moodle from 1.9 to 2.2 to 2.5.
Everything upgraded fine except few videos in a course didn't show the video player at all. I looked up at Media FAQ and changed the player size by adding ?d=400x300 at the end. The Video Player showed up .
Clicked on the play button, the video shows up but its very very very small!
I have also attached a sample.
That is really odd. I have never seen that before. Sometimes when I start to play a video that I have recorded on ipad and converted, it looks like that, but it pops into the right size almost immediately.
I looked it up and came across this:
http://flash.flowplayer.org/forum/2/78777
I am not sure if that helps, but possibly your video was not encoded correctly and different versions of Flowplayer are more fault tolerant. I would try re encoding the video and see if it makes a difference.