I don't have an AJA card or the drivers installed, but my guess is that that's just the way this command is wired; it's assuming that you want to use the hardware for monitoring/output, which as you know, requires you to use an AJA editing mode.
This is one of the weird things about this command/feature, and frankly, one of the reasons I rarely use it. In general, I find it's not the best guesser about what editing mode to use--it's a lot smarter in CS5.5 than it was in CS5, though. It typically picks the correct parameters--frame size, for example--but occasionally it assigns a bizarro editing mode. Personally, my preference would be that it always defaulted to the Custom editing mode, but maybe that's just me...
So... ahh... what's that thing I say again?
Cool. In the interim, if you have a few different sequences that you'd like to quickly create, take the time to create and save your own sequence presets. It won't take much longer to open the New Sequence dialog and apply one of those, with the added benefit that you always get what you want, and you're not just playing the Mega Ball New Sequence Lottery!