Thanks for the suggestions.
I hadn't realised that "embedded browser" meant operating system browser: http://www-01.ibm.com/support/docview.wss?uid=swg21282102
By setting Disable embedded browser for MIME email we will be disabling the use of the operating system browser (in this case IE11) and reverting to the Notes browser.
The setting does work and gets us around the issue however it does not explain why we need to use the Notes browser instead of IE11 when we didn't with IE9. We have an open PMR with IBM and hopefully will get an answer.