So I did the automatic update of frame market.
My sites got invalid function call errors. I was told I probably hadn't got all the files. So I delete framemarket and download it from WPMU and reinstall it.
After faffing around I get gridmarket to show up again and I activate it.
Now not a single one of my sites is using gridmarket, and when I switch them back to it, they have lost all the settings my users have put it.
I had make some changes to the gridmarket theme, but nothing major.
EDIT: It seems it was the changes I made to gridmarket. They were fine before but now they are causing problems. I thought I could make changes to a child theme and still be able to update safely.