Applying for a PhD in Engineering. Crappy Undergrad GPA, Good Masters GPA. Help!
I would find the second Master's Degree very helpful. First, because its shows that the 3.6 GPA on the first Master's was not a "fluke," and second, because it is actually higher than your first Master's, showing "improvement." And the first Master's shows improvement over your last two years of Bachelor's which is an improvement over your first two years. 

In your shoes, I would send people the last six (or five and a half) years of grades. That is your two Master's years of grades. plus the last two of your undergraduate. That's also the equivalent of what someone with four year's of Bachelor's, and one and half year of Master's work will show.

But the most encouraging thing about your record is your steady improvement. Many schools would be willing to overlook a lot of C's in your first two years of Bachelor work, as a result. They're more interested in the last four years of "A" level Master's work, as well as the 3.5 "bridge" in your junior and senior years.