I've been doing a lot of reading around this issue, in particular similar issues with other devices.
The conclusion I have come too is that my Samsung LE40R87BD is capable of displaying PAL60. So it looks like the AppleTV is sensing the maximum refresh rate possible by my TV and defaulting to that. Until Apple make the mode selectable like the old AppleTV, then the only option seems to be switching off PAL60 in the TV settings. The only problem with this is you can't! However I have found the hidden service menu which has lots of additional options, and I am going to wade through to see if I can find anything relevant. I will post anything I find.
Thanks everyone for posting their experiences.