Hi stevenminix, thanks for using my plugin.
The iframe is a different method to embed a video and it is normal that it doesn’t keep your logo and your player skin; actually, the player itself is not the same.
At the moment, the measures of the iframe are fixed to 640x360px, and it’s not possible to change them from the admin page.
If you need to do it, go to your plugin folder/includes/jwppp-functions.php around the line 870, and find the follow line:
$output .= "code: '<iframe src=\"" . $jwppp_embed_url . "\" width=\"640\" height=\"360\" frameborder=\"0\" scrolling=\"auto\"></iframe>'\n";
Here you can change the measures as you need.
Hope this helps.