I hear that about Cherryh a lot, but I think it has more to do with the development of her voice as a writer than a difference between her SF and fantasy. That is, the Morgaine cycle (well, not Exile's Gate) and the Ealdwood book(s) are from very early in her career, when her science fiction (Hunter of Worlds, etc) wasn't all that different. Downbelow Station is much more similar in tone to her early fantasy than Finity's End, and FE is the sequel to DBS.
I think her series can appear uneven because she has a habit of writing a stand alone book years later. Chanur's Legacy, Exile's Gate, Fortress of Ice and Regenisis were all published years after the trilogies they continue, so reading them one after the other can be a bit jarring. I had the same experience with the Fafhrd and Grey Mouser series, which are always collected in chronological order; there are 3 or 4 stories about their early adventures, so when I get to "The Jewels in the Forest," the first story Leiber actually wrote, I always feel like he had stroke or something.
I'm really curious as to Dan's opinion of the fortress books, because Fortress in the Eye of Time was written right around the same time as Foreigner. Of course, that was about 20 years ago, so her voice has developed as she's been writing that series.