Have you tried putting things into the bag to see how the lining fits? Bosal foam interfacing is heavier than Soft and Stable. It could be that the heavy fabric is weighing down the interfacing. More quilting will also make a sturdier bag. Did you use the foam interfacing on the vinyl too? If not, the heaviness of the top quilted part may be causing the vinyl to sag. Also, be very careful sewing vinyl. Too short or tight a stitch can cause it to tear when pressure (or in this case, weight from whatever you are putting in the bag) just like the serrated edge on a box of plastic wrap.
I have had the same problem with linings and usually 'dry fit' and tweak the lining before sewing it all together. I have sometimes quilted the foam interfacing to the lining and then made the outer to fit over top. Sort of backwards but it works better for some projects.