The Windows version has more options. You should be able to get it to display very similarly to what the Cybook does if you play with fonts and other options, but the reverse isn't necessarily the case (some things that the Windows version can do that the Cybook version can't do).
There are also differences in underlying capabilities, but these are typically only significant for reference works like some dictionaries.
If there is some capability in particular that seems to be missing, I suggest posting a screenshot of the Windows version, see
HowTo (use "Alt - Print Screen" on the MobiPocket window) .