I changed the location of the file in iDisk, and it seemed to fix it on both the iPhone, and on my mac. I don't know if the problem was the file on iDisk, or if it is something to do with having it it in the Documents folder. Here is what I did:
On my iDisk, I created a new folder ie: OmniFocus. (make sure its actually on the server by either doing it at me.com, or syncing your iDisk from your mac.)
In OmniFocus on my mac, I changed the location in the Preferences->Sync->MobileMe to the new folder:
https://idisk.me.com/USERNAME/OmniFocus/
Then I synced OmniFocus on my mac.
After it was successful, I went into OmniFocus on my iPhone, opened the settings->get settings from Mac. On my Mac, clicked share settings. When the iPhone sees the settings, selected it.
iPhone synced just fine, and so far, so good.
Hope this helps.