Version 1.31+ should automatically set these settings for you.
Unchecked YT Center Settings > Player > Player Size > Enable Resize.
Unchecked YT Center Settings > Player > General > Scroll to Video. YT Center will scroll to the wrong location.
The HTML5 player was only designed to be sized at 640px or 848px wide. Thus, the progress bar will not be resized. Using the flash player will "fix" this.
Screenshots
After loading the video webpage you will see:
It appears above the rest of the site, so you can scroll down for the description, related links, etc.
Changelog
1.41 - Aug 11, 2014
Remove poorly done HTML5 fix. The HTML5 progress bar will remain unfixed until a Youtube update provides the ability to resize it.
Use CSS absolutly positioning to move the player. This should fix playback restarting while moving the player.