The closest standard, even though it has been superseded was MIL-A-8625.
As for the issues that you have been experiencing, there are some things that could cause them:
1. Improper cleaning before they left your company
2. Improper cleaning at the supplier providing the service
3. Machining roughness
These are just some of the causes, in my opinion.
One thing to remember is that when parts are sent to anodizing they will only enhance what may be wrong.
There are a few things that you can consider:
The supplier of the service has specific steps to apply the anodizing coat: They are required to clean, dry, etch, apply the coat and rinse. They are also required to change water (both the rinse bath and the anodizing bath). If this isn't followed, it could add contamination/discoloration to the product.