Why does Drop Box not work after 10.8 upgrade?
To be honest it sounds like it could be a bug in DropBox, and you should contact them to find a solution (and please post the solution here if they give you one).

Why do you have the DropBox folder on the server? Why not have a dropbox folder on the server and a completely separate one on your notebook?

Perhaps it's not what you want, but it seems like that should work perfectly. DropBox usually sends files across to the other machine within a few seconds.