Doh! Well done you guys, you sussed out the obvious mistake! Yes I was running Blackberry Manager from an old desktop shortcut. The new Blackberry Manager works fine.
I hadn't realised the Manager was all new in 4.1 and in fairness, the upgrade docs didn't make that clear if indeed they even mentioned it. Don't see the point of having the Legacy Blackberry Manager there at all, can only cause confusion!
Thanks for that one, looks like the upgrade was a total success now that's all sorted out.