The colors and the note style of the active theme should be synchronized between all computers. The saved themes are not (I think this the same as Version 8).
As an example, if I create a new theme on one computer, save it and then synchronize, the other computers should all select the same fonts, colors and note colors as the one I designed the theme on (after they have successfully synchronized). However, on the computers I didn't design and save the theme on, the theme would not be added to the list of saved themes. In version 9, they have recently added the ability to export and import a theme. So there are two ways to transfer themes. What I have been doing after creating a theme is Save it on the computer I created it on (A). Then sync. Then on the computer I haven't created it on (B), after the sync it will have the new Theme settings. I then go and save it as a new theme. What I also do now is export the theme and attach the file to a thought with the Theme name and a screenshot. Then when the brain is synchronized I can open that theme on any computer which doesn't have it in the list and copy the file to a different location and then import it. This method works well for me, and I'm a fairly active theme user/creator. Hope this helps!