Was able to get some assistance from Kofax the owners of Readsoft (thanks for the help).
This problem has been reported to Microsoft but no fix has yet been made.
The only way to make the OCR service setup sync masterdata is that each BC company has a unique "Customer" set up in Readsoft.
Then this should work. I've not tested this since this is not an ok solution for the product I work.
The issue with that solution is that anyone that login to readsoft will need a unique login for every company. Which may be alright for customers with only one BC company but if you have 10 companies and have to login for every single one then it can become tedious.
We decided to extend and change the masterdata sync functionality with an extra required setting (Buyer ID) this has made our sync work well.
So no official solution currently available.