Domain / Subdomain Issue Update

The way long-time users who went from a subdomain to domain/subdomain arrangement are set up, it appears that we are using data from the domain to load pages from both. I say this because:
- I never update the subdomain, but it stays the same as the domain
- Webmaster Tools is systematically voided my verifications and is assigning new code. This is consistent with having both codes on one site tripping a doorway or duplication of content issue with Google
- It doesn't make sense that the WT code should be installed on sub and domain in the same window and cannot coexist beyond initial verification
- Since becoming deverified, my Google Analytics reports are identical for domain and subdomain.
- My results are falling in SERPs results, suggesting a penalty has been administered

I don't know whether they are double counting traffic, but since accurate analytics are at the heart of any web business, not having them, or worse, having deceptive numbers, is a major setback.

Someone knows how Google is viewing these sites, and that needs to be explained to allow implementation of remedies.