There is no reason to run a frame limiter unless you're getting screen tearing. That includes vsync. Just turn it off.
With a multi-gpu setup, vsync is actually going to make micro-stutter worse. You need to adjust your settings accordingly. I like to keep my average fps ~90 to account for dips; I start seeing micro-stutter at ~50fps, so I don't like my minimum fps to ever drop below that. Also, if both of your cards are always at 100% usage, you're going to see micro-stutter more often. I don't know what settings you're running at or what your gpu usage is, but you may want to turn MSAA down/off and see if that helps. I think a lot of BF3 micro-stutter is driver related, but until that gets worked out, you may have to turn down a setting or two.