Hello Pete.
IE9 is not officially supported in Kentico
CMS 5.5R2, as you can see in system requirements for this version. Still, we fixed many issues in hotfixes, however when having some problem in IE9 even on version with the latest hotfix, you will need to use a different browser, compatibility mode or upgrade to 6.0. Thank you.
Best Regards,
Radek Macalik