I came across this today. I came up with a filthy hack fix to force crop both thumb size and medium size images.
This is for 2.5.2:
Just get into wp-includes/media.php and go to line 148 and add the following code as the first line in the function image_resize_dimensions:
$crop=true;
That’ll force the issue of the crop. I am about to write a plugin that’ll set up the ability to just check a box in the settings menu of the admin section, but until then a filthy hack…