no problem.
setting a preferred form won't bypass permissions issues, but I still don't think this is it if the person trying to print the check can see the data.
it seems like you might be on to something with the store form with record checkbox on the form. If the old records were stored with the standard form, you'd have to edit the record, change the custom form to the one you want, then click save, this will save the record with the new form. storing a record with a form will override the preferred form. After updating this you can try reprinting to see if this fixes your problem. Clicking edit on a record and seeing what value shows up in the custom form field is the easiest way to see what form is currently being used.
I don't see you addressing batch printing vs one-off printing. But, based on your answers, i'm assuming you are talking about one-off printing.
As an aside, an issue we had when printing our voucher checks was that the only way we could print a single record to see/use the template I created was to click edit and then select "save & print". Clicking the print icon on the record when in view mode didn't result in what we wanted which was really annoying.