This could be due to the new OmniFocus sync format that was introduced with OmniFocus 2.6.1.
New OmniFocus Sync Format
Beginning of August, Omni has released a new version of OmniFocus (2.6.1 for Mac, 2.15 for iOS) which supports a new encrypted sync format.
FocusGTD 2.5.2 (and higher) are required to support encrypted sync.
Watch Google+ for news about FocusGTD support for the new format.
How do I know if I already migrated?
Open OmniFocus for Mac and check the File menu. If the option “Migrate Database” is greyed out, then you have already migrated.
I don’t have a separate sync password but I still have problems synching
Please contact support at focusgtdapp.com in order to get help.