I have an application that I ported from the legacy daq to session based. No problems using the legacy interface to the desired speed. I use an encoder channel as an external clock to trigger a/d samples. It works up to approximately 1/3 the speed that it should work at and then starts dropping measurements. I am wondering if the toolbox code sets the digital filtering for these inputs, but I see no way to tell that.
I am using 2012b. Thinking about trying 2013a, but haven't gotten around to that yet.