I found that while the problem existed I simply had to re-save a few settings to keep my theme as I wanted, then recently with the latest update of Gantry everything works fine (a few space bars moved when I upgraded but easily fixed, plus the iPhone theme has a small problem, but on the case).
I'm a little easy on these guys because I get a hell of a lot out of these products for what I see as very little money, these themes are some of the best out there and something like Gantry is a complex beast that solves a lot of Wordpress shortfalls. I knew that If I was patient the problems would get sorted out and they have.
There's a human on the other side of this forum, treat them nicely