Sorry confused here, how long have you been doing the books on CB? For example did you keep the books on CB last quarter but submit the return elsewhere? or where the books kept on another system up to the last quarter?
If you've lots of historic data on CB but have never processed a VAT return on CB, ie created a return (whether submitted or not), then if you now create a return and tick that box, it will assume none of the previous entries have ever been on a return and so bring them all into the new quarter.
In such situations people usually create returns in CB just to mark the entries as having been returned and stopping them from being brought into later returns with the tick box.
So in normal circumstances, also being on cash accounting, if I did my last return to 31 December without having processed a few payments they would have been missed from the December return. If I now go back and process those payments (from pre 31 December) it creates virgin VAT entries in the VAT control account and so, when I do the March return AND tick the box, they will appear on that return.