I'm using the latest version of NextGen (2.0.40).
On sites where I have the theme set to Canvas (WooThemes) and am using the boxed layout option, when I turn on the NextGen plugin the layout of the site is messed up and I lose the padding down the left and right edges of the site. Here are a couple of pics to highlight the problem:
Before NextGen is activated:
Also, from playing about with the theme settings I've discovered that this only happens when the "Enable Fixed Mobile Layout" is checked.