I´m having this weir issue with objects that have gradients with opacity.
If I drag to copy, it´s makes a perfect copy. But if I copy/paste the object it becomes solid. This applys copy/paste in the same document and if I try to copy/paste into a new document.
This problem came with the upgrade to Illustrator CS6.
Mac OSX 10.7.5
Adobe Illustrator 16.0.4
Just to rule out preference corruption in CS6, you may try to Move the folder (more thorough and reversible) with Illy closed, or Cmd+Option+Shift during startup (easy but irreversible). You may prefer the former, especially if you like your customized settings.