We've been working on setting the correct active/bypass state on presets before transferring them over via H9 Control. (See http://forum.eventide.com/cs/forums/t/9091.aspx) This should fix the problem you're seeing.
In any case for now, if you correct the active/bypass state for the preset and resave it directly on the H9 as described in the H9's Quick Start Guide among other places, that should also fix the problem. Could you give that a try with one or two presets and see if that works?
