A variant does not save report data - rather it saves the report 'look and feel' - the displayed coplumns, their order, the sort and filter criteria etc. Your check boxes are basically data.
I would look at possibly inheriting the tree into a local class and redefining the load and save variant methods (if you can find them) to load and save your checkbox selections as well. Don't forget to call the Super methods though.
Regards
Rich