Thanks Eddie, that was it. Thanks for the speedy reply to this.
I'm very suprised that this option is unticked by default.
Personally, if I take the time to place a column in relation to its function and related columns then I want this metadata to be carried through by SQL-Compare. I can't think of a situation when I wouldn't.
Additionally, if I had code which used ordinal column numbers for sort or grouping criteria then SQL Compare would actually break the application by possibly returning the results in the wrong order and it would be very difficult to trace as it would be non-reproducible at source.
Please pass these comments on to the development team at RedGate.