The height/width is written into the database on every upload through add media=>wordtube. That seems to cause this behaviour.
Fixed it for me by changing/hacking the following code in file
$act_width = 0; // change from 320 to 0
$act_height = 0; // change from 240 to 0
line 93-94: (add doubleslashes to those lines or delete them)
// if ($act_height < 20 ) $act_height = 20 ;
// if ($act_width == 0 ) $act_width = 320 ;
Then the default values set in the options menu will be taken.
Strange why this problem is still in the code.
Be aware that I did not test properly therefore I am sure there will be side-effects with other filetypes or whatever. But for .flv movies this works in the normal player.