Oh, I've just realised that chucking away the AME prefs from (below) has solved the problem. Someone mentioned chucking away prefs in another thread but I must have chucked the wrong ones. So, if anyone else has this problem then try this...
USER Library > Preferences > Adobe > Adobe Media Encoder (chucked this whole folder way containing 5.5 and 6 prefs). New ones were made and both working perfectly