You must have selected under Preferences ==> Behavior to use the calibre internal viewer for PDF. Uncheck that option.
By default calibre passes PDF on to the system PDF viewer, which should work much better.
Also, Kovid recommends against using the distro version of calibre, which is usually going to be out of date. calibre is updated weekly. L/X/Ed/Ubuntu 13.10 has version 1.0.0, we are now 34 weeks and 34 versions full of bugfixes and several major new features past that. Download the latest version here:
http://calibre-ebook.com/download_linux
Everyone makes this mistake their first time with linux.