Altium V15 - Dup designators that won't fix on board level annotate

[Psi]

So I have a schematic that uses many device sheets, some device sheets use other device sheets.

The issue I'm having is in trying to get the designators all unique using board level annotate.
The process does not seem to work right, once its done there are still many dups that it creates.

Have tried "reset schematic designers" and reapplying them, no change.

I have tried resetting unique identifiers, there were some dups that got fixed.

Any ideas?

[Psi]

I also get some odd errors like  "Duplicate net names wire NetF5_2"

This is for a wire that I have not give a manual net name, its giving its own internal net name to that net and for some reason its giving two nets the same name then complaining about it.

[ajb]

The duplicate net name may have to do with how you have the project structured.  Altium isn't very sophisticated about how it compiles net names across multi instance sheet symbols, so there are some ways to set up sheets and connectivity between them that will confound it.  It's entirely possible that whatever is causing the duplicate net names is also causing the designator problems, so you might want to try to resolve that first.

As for the board level annotate, you might need to delete the annotation file from the project and start over once you get.any underlying issues resolved. 

[Psi]

As for the board level annotate, you might need to delete the annotation file from the project and start over once you get.any underlying issues resolved.

yeah, I've tried deleting that file but no luck. Definitely still an issue somewhere.

I think I will make a copy of the project and just start deleting sections, see if I can do a binary search and locate any problem area. Assuming it is a specific area causing the issue.
The dup designators themselves don't seem to be limited to any section but it's hard to tell exactly.