VM....did you cook them at a lower temp because of the glass dish? Was the glass dish a 9x13? If it was a bit smaller, your bars were deeper and that's why they didn't cook completely through.
If you want them done a bit more, you could pop them back in the oven for about 3-4 minutes at 325, if they are only slightly underdone. 5 minutes if they are closer to raw in the middle.
Best to bake them in an aluminum 9x13.
I always make my cookies with real butter rather than Crisco or margarine. Makes them a wee bit flatter, but I would rather have them flatter than eat margarine or Crisco.