Sync 2 to 3 upgrade GPS is way off

Help please guys, I retrofitted my 2014 Raptor with sync 3 and had everything working as it should, then the truck went into the dealership and now its all out of whack. I can get the GPS clock to update, but the navigation can be off by upto a mile away, When I get the navigation to work correctly the GPS clock wont update, I sure I have something wrong in the apim but for the life of me I cant figure it out at present

SYNC Region: NA

Navigation Variant: Nav

Manufacturer Year: Pre MY20

Install Type: Retrofit

Old SYNC Version: 3.4

New SYNC Version: 3.4

Do you have a error message, if so what is it?
Sometimes it shows navigation fault

Update Method: CyanLabs Syn3 Updater

Syn3 Updater Version: I really dont remeber

Syn3 Updater Documentation Read: yes

Syn3 Updater Log File

Dont have one

try a master reset

What did they do?.
No healthy APIM behaves like that without a reason.

If you have your previous as-built values saved, re apply them.