There seems to be a small bug in Sorenson 4. In some tests done by Graeme, Jens and myself we found that when you choose a preset flv encoding profile then the metadata inside the produced flv shows width AND height set to the WIDTH of the specified profile even when the profile has settings that show different numbers for width and height.

Example: if a profile has output of 240×180 then the metadata will incorrectly show 240×240.

This can cause problems when trying to replay with a flv player that relies on metadata to scale the video to the correct size – and all players I know do that.
Sorenson confirmed to me that there is an issue as several people had reported it.

It could well be that if you create a custom profile then the error does not occur but I am not sure. All I can say is that sometimes (maybe all the time) the width and height metadata is incorrect (strictly speaking the width is correct but the height is not).

Sorenson said there is no immediate fix and they try and correct this in a point release.