It appears the culprit is the All In One SEO Pack plugins (both pro and free versions)
I will see what they have to say about it however I am certainly considering converting to Yoast despite cost difference. The cost is small in comparison to the time spent finding these issues.
I am well aware from cross referencing a heap of info that Yoast SEO is optimized to work best with other top plugins that are also optimized to work in conjunction with WordPress SEO like W3 Total Cache for example.
It is entirely probable that the AIOSEO plugin has been why the set up on W3 Total cache has been a bit problematic. I thought (being the hopeful sort) that it may just be due to it not being entirely version compatible but maybe its been AIOSEO plugin the entire time.
Time will reveal all, no doubt.