It’s not impossible, there really is no such thing as flawless synchronisation, so maybe something is glitched on their server and isn’t recovering gracefully. It would be unlikely though. The main trigger for this, by the way, is the “user.lock” file inside the project bundle, under the Files directory. If for some reason Dropbox is not cleanly removing that file when you quit, that would cause the program to think it’s still open.
Well, sorta. The time between using computer A and computer B is less important than getting a clean and full upload/download while still on A or B. In other words, if I shut down the Mac with the Apple menu while Scrivener is open, chances are extremely high that everything will be closed before Dropbox even gets a chance to upload the last set of changes you made (like removing that lock file). Even if you wait ten years to open it on the second computer, Dropbox will never know there was a last batch of changes pending on the first computer.
Same thing can happen in inverse on machine B. If you fire it up and instantly open your project while Dropbox is still downloading the latest version, you’d actually end up loading a partial copy of the changed project since your local computer is completely up to date from the server yet.
I’d suspect the first problem though, based on your description. It’s more likely you are shutting down to quickly on both computers and so the last set of edits aren’t on Dropbox at all. If you do this a lot, you’ll end up with a bunch of “Conflicted” files in the bundle which can, over time, lead to instability (a problem which can be reversed with a little diligent manual labour of going through all the conflicted files and erasing everything but the latest copy of each one, and renaming it to not have the parenthetical that Dropbox adds, if the conflicted copy is the most recent).
To avoid this, quit Scrivener and then shut down the computer only after the Dropbox icon in the menu bar has stopped “spinning” and has a green checkmark beside it (or if you are using the black and white theme, when it looks like a solid box, sans any animations).
I’ve never actually tried doing that, but it wouldn’t surprise me if that causes Dropbox to re-download everything from scratch, regarding the machine as a “new” computer in the network—so you’d have the same problem if you did that and then quickly tried to do something in that folder. Even worse, because a full download could take hours rather than seconds.