He, I know I'm old school and all... the station I work for is still in SD... we are using Kona LSe cards, using mainly FCP. Though the new additions to CS5 make me want to work with it..
and this is a big fat BUT...
When I start an AJA Project, the timeline is ridiculously jerky. HD DSLR is smooth as silk, but AJA is almost impossible to edit in.
Of course there are many variables involved here, but the directly supported file types should play back in real-time with no problem in SD, almost regardless of the disk system you're using. Try contacting our support department and they can run you through some troubleshooting to try to get to the bottom of the issue.