Themes need to be developed both specifically for your model of iPad AND for the version of IOS which you are running.
Themes work by replacing the graphics in IOS with alternative "themed" versions. When Apple changes the name of an icon or graphic within IOS, which they do with EVERY new major and minor release of IOS, then those items will cease to be themed until the developer of the theme changes the name in the same way.
Unfortunately, the theme you are using has not been updated for 5.1.1, so until it is, you are going to experience a lot of issues with it!
Check our themes section which usually gets updated with details when popular iPad themes get a release - iPad Themes
Hope that clarifies! (oh, and welcome to the forums!)
Thank you very much. I've just bought 2UInique, and it works, but Photo Booth and Contacts aren't skinned (waiting for an update); and InPulse also works. Thanks again