So, your concern is that when you graduate with a Masters in Financial Engineering you will be low balled on your starting salary because your work experience prior to entering the Masters program was not directly related to Financial Engineering...

Well, heres the deal, most people who graduate from a Masters Program in Financial Engineering don't even work in finance, let alone have work experience working with derivative products. Here are the prior employment stats for the most recent entering class at UCB (one of the top 3 programs in the world)

Engineering: 14%
Marketing/Sales: 2%
Information Systems: 10%
General Management: 2%
Finance: 20%
Research & Development: 17%
Project Management: 0%
Consulting/Management Services: 8%
Planning: 2%
Education: 10%
Other: 15%

As you can see, 80% of the class did not work in finance.

Theres a reason that most people who do not have a Masters in Financial engineering have absoluty no experience with derivatives. The reason is that, derivative products are VERY risky, and VERY complicated. For these two reasons no company will let anyone other than someone with extensive specialized education even approach derivatives.

So, your experience as an analyst will not necessarily place you at a disadvantage. The skills needed for Financial Engineering are quantitative, prove that you are going to be the one to come up with the next big formulae and you will suceede.