In Apex 4.2 (not sure about other versions), there can be extra white space to the right of the page when using checkboxes and/or radio buttons. This causes a horizontal scrollbar to appear - in Firefox and Internet Explorer anyway, Chrome seems to be immune.
This behaviour is caused by the width:100% entry in the "legend" css class defined in the Bootstrap css.
Paul Broughton wrote a nice article on this: http://www.paulbroughton.co.uk/2012/12/twitter-bootstrap-checkboxes-and-apex-42.html
I opted for a slightly different solution, that does not require editing the original Bootstrap css file.
I added this to the Page Template (in the Cascading Style Sheet -> Inline section):