I left a comment on the main blog as well, not sure if OP is blog author:
I think users may want to proceed with caution:
How do you get around the files DropBox makes not colliding? If you look at a default install, just one instance, view all files in ~ using something like ls -la and you will see a pid file, some caches, some SQLite DB files, all hidden from Finder view.
Then there are the preference files and others stored in Application Support and Preferences, plus possible launchd items as well. Also Contextual Menu Modules that need to know the active user ID. You may find your public share URL's don't work or share the wrong paths.
It seems the second instance is going to stomp on the files of the first. I can estimate why it works in the beginning, as much data may be resident in memory. One app will always load first no matter what.
I think over time this may start to fail.
One suggestion to possibly make this a little cleaner, assuming it does continue to work, is put the call to launch the app into Automator for both apps. Then you are only adding one item to your startup items and never even launching the DropBox app directly from their package .app launcher.
Or, you could dig into the package and edit the startup paths there, but you probably will want to stay outside the .app bundle for update reasons. Updates would nuke those changes.
I think launching both from one Automator action is the cleanest. Though I am curious, for example, the black and white icon versus color. Those are stored as preference values. Can you look on your system to see where they are stored, and how DropBox is now storing two separate values? Does it do it in the same file or somehow magically create a separate file and know where to go looking for it?
There is a .dropbox folder in the HOME folder (whatever that is set to). It contains the following files:
$ file *
config.db: SQLite 3.x database
dropbox.pid: ASCII text, with no line terminators
host.db: ASCII text
host.dbx: ASCII text
photo.dbx: SysEx File -
config.db doesn't contain any interesting information, the directory "l" is empty, and I can't easily get any information out of the other files. It doesn't seem unlikely that all preferences are stored here, though.
Still, running both instances from a non-default HOME seems like sound advice.