I've had the same problem and this is how I got around it, hope this helps.
Calibre by default puts all the transferred books in the iriver story "book" directory. But for some reason my iriver story doesn't list them when I press the BOOKS button. I have to navigate to them using MY FOLDER. And therefore I can't search, bookmark or use favourites.
BUT....
if I move all my book folders using windows explorer to the Adobe Digital Editions folder on the iriver, then everything works as it should. (not sure whether you need to connect the story to digital editions first just to activate it - I'd already done that - but I hated using digital editions, so I switched to calibre)
but then calibre doesn't see whats on the device because it looks at a different directory. So I disabled the iriver story plugin (in calibre preferences, plugins, device interfaces). And also edited the "Folder device interface" to have the same settings as the "iriver device interface". You have to restart calibre for the new settings to take effect.
Now whenever I connect my iriver to the computer, I click "Connect/Share" in Calibre, and "Connect to folder". Then I choose the adobe digital editions folder on the iriver story . Calibre remembers the folder setting after the first time. And Calibre now works perfectly with my device.
Something else I did to fix an annoyance with the way the iriver lists books was to chance the "Save template" on the "folder device interface" to :
{author_sort}/{series}{series_index:0>2s| |-}{title}-{authors}
That puts each book into the author folder, with the series, then title, then author. Its personal preference but I just find it easier to see the books that way.
cheers
