Posted by Mr. Q at 6:00 AM Monday, September 17, 2012
Long Question; Short Answer Dept. You need to see an IP attorney. We believe the letter granting all rights will trump prior agreements but we couldn't say for sure without looking at the papers. If you're still interested in patenting the invention, you need to confirm your ownership and you also need to check your deadlines particularly if the invention has been disclosed or published. Here's a collection of articles that may help you sort out ownership issues and here's a previous entry relevant for California inventor-employees.
BTW, speaking of inventors, today (actually yesterday) marks the one-year anniversary of the America Invents Act and seven provisions of the AIA go into effect: inventor's oath or declaration; preissuance submissions; supplemental examination; citation of patent owner claim scope statements; post grant review; inter partes review; and covered business method review. Read more about it at our AIA timeline.