I was on the phone with tech support this morning and asked the same question. The answer is 'yes', but you have to make a copy of the executable and run it as a separate program.
The problem is that Media Express only allows one instance of the software (this would be nice for BlackMagic to change), so you have to trick it into starting two instances by having two completely separate executables.
At that point, you should be able to open the two copies separately, select the different devices, and do two captures.
I haven't tried this yet as we're still testing our first H.264 ProRecorder. If you have the chance to try it, I would love to hear how it goes before we invest in a second one.