Thanks Tim,
I have tried creating a new file GDB with a new featureclass, tried old personal (.mdb) GDB's, tried upgrading them to current version, tried having the data in a feature dataset and not in one, tried someone elses computer, have re-installed arcgis and arcpad.
Tried text based definition query, number based def query, data on local drive, data on network drive, .mxd with only 1 layer in it then tried all these things again. No joy, every time it ignores the definition query and exports the whole lot.
I'm very over it. One thing left to try. I'll try and get hold of Desktop SP2.