as mentioned above, I didn't have problems syncing the preferences to a second machine - in my setup simply enabling the sync feature on one single Mac reset all my settings which should have been synced and I was unable to permanently change stuff from that point on.
So I tried again with v2.0 build 131 - but to no avail.
As it turned out, the problem actually was a Dropbox problem, but nothing that could have been changed by waiting for a complete dropbox sync: I thought it would be a good idea to use a subfolder of the Dropbox "Apps" folder for keeping the Alfred prefs - a bad idea, as Dropbox is somewhat picky about this kind of special folder...
The "Apps" folder on your Dropbox root is the designated place for external programs using the Dropbox-API to place shared content. Maybe you already tried some iOS-App with Dropbox support - normally these programs request either full access to your Dropbox or only limited access to its own folder (inside the "Apps" folder); if you grant it, you'll receive an email ("...you've connected a new app to Dropbox. Awesome!") and find this app inside your Dropbox setting under "My apps".
So there obviously is some magic going on with this special Dropbox location: reproducible and independent of the name ("Alfred 2", "Alfred2", "Alfredo", ...) of the subfolder I choose for the Alfred preferences: if I put it inside ~/Dropbox/Apps/ the prefs get corrupted and Alfred is unable to keep the settings.
I now chose an "Alfred 2" folder directly under my Dropbox root and everything works as expected. So my advice: stay away from your "Apps"-Dropbox-folder...
Gargamel got a reaction from Maverick in ~/Dropbox folder syncing issue [In Progress]