Here's the thing; OmniFocus' built in syncing is an item-level sync. So an update to a few items on one client and updates to a few other items on another client get merged on each sync. It even handles conflict situations wherein the same item gets updated on multiple clients before being sync'd.
When you do any other kind of syncing, you lose this intelligence. Instead you have a file-level sync. So File A overwrites File B. This gets even more complicated, because OmniFocus' document is actually a package containing lots of tiny documents (like a digital Russian nesting doll). So many sync processes will end up merging those internal files, which causes no end of craziness. DropBox is one such sync'ing agent.
If you want to roll your own sync and do a file-level sync, you are going to have to be VERY careful, and follow this process EVERY TIME you use OmniFocus:
1. Sync to server
2. Open OF, do your thing
3. Close OmniFocus
4. Sync to server
If you do not follow this procedure every time, you will end up with conflicts. Conflicts will lose data.
As I mentioned in the post that spawned this one (according to the PM you sent me), in order to get DropBox to work, I also created certain scripts that would force a remote OmniFocus session to quit.
My advice: Stick with WebDAV/Mobile Me or Bonjour syncing. Omni's done a great job with the syncing process. Unless you're as anal retentive about technical stuff as I am, you're just inviting pain.
Check out
this post for information on alternate syncing arrangements that might make your life easier. The one I'm using is quite stupidly complex, and I cannot recommend it to anyone else, even though it does set a nice balance between speed and ubiquity.