Hi there
I’m hoping this might be helpful. I am using Portfolio Press 1.5 on WP 3.5.1 and have been trying to work out why it was happening to me too with portfolio post type items. Within Appearance > Theme options > General Settings there is an option Display Images on Portfolio Posts that when unchecked does not automatically display the featured image… you can then add a different image into the post without duplication:
See the FAQs at the bottom: https://wptheming.com/2010/07/portfolio-theme/
So you therefore need two images in this case, one for the featured image with a decent crop and the main full size image. A bit of a faff but it seems to get round the issue…good luck ??