A little, but not enougth to make that much of a difference. But with that many fans blowing on the heatsink I'm not supprised you've got problems!
Before I get into this; be sure you have the fan mounted in the same direction as before. You want a clear unobstructed flow of air from the front intakes of the case through the processor and out the back. For this you want a linear flow of air; turbulent flows cause no end of complications. Unfortunately when you pull air in different directions like this its what your going to get.
This is largely guesswork on my behalf, but this is what your airflows used to look like:
A few things to remember. First, air is a fluid and so obeys certain rules such as always seeking the easiest path to flow along (path of least resistance). Second, having good airflow across your RAM isn't a bad thing. That Giel stuff runs at 2.1V and it has a heatspreader for a reason.
With your new fan position it'll look a little like this:
What’s happening here is that the suction from the 200mm flow is pulling air away from the bottom part of the heatsink, meaning in the red area the air is moving slower (note; it is still moving). The air for the cases back fan is taking the easier route around the heatsink rather then through it. Obviously this isn't using your heatsink that efficiently!
Now the problem with your first setup is that your fans weren’t running very efficiently. Using two instead of one might mean you can half the load on both, but you'll always be generating more noise then one. It would be better to remove the case fan have some sort of ducting to channel the hot air to the out-take.
The problem with the second set-up is that the larger fan is disrupting your airflow, and although the air is moving quicker it isn't doing so more efficiently.
My advice would be to keep the 200mm fan on its lowest setting, or turn it off altogether. Keep the rear fan on Medium or High to help it keep up with the processor fan. Do some benchmarking with stress-tests to see if it makes a difference.
Again; this is guesswork. Complex airflows are very difficult to model outside a lab.