[Falkirk]

I'm not sure what you have is a synching problem.

I only have the iPhone version of OmniFocus. I do not sync at all but I too have a problem with the creation of multiple Miscellaneous folders. The extra folder is obviously created when I create tasks but other than that I have been unable to discover a specific pattern.

You might want to consider looking for somewhere other than the sync function for a solution to your issue.