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If it's a commonly used acronym then both the full keyword phrase and the accronym should be included in the SEO optimization process.

Moz doesn't check only on the title or other meta tags. You could have an entirely different title and if the page content is the same it will bring up a duplicate content flag. As an example, on our blog we had duplicate content alerts between categories and tag pages (ie Category page 2 had the same content as tag page 20). Instead of changing the contents of the pages (as it was nearly impossible) we decided to add a meta noindex to the tag pages. All duplicate content issues resolved Anyway, Moz crawls your page once a week, if you did the changes recently, check the date of the last crawl under your campaign overview.

Lastly, I've been using this pattern in regards to meta tag titles... company name | description Since all the descriptions are unique, would it still be considered a duplicate, given that I'm always including the company name?

I too was confused by the question. Can you explain in more detail what your outsourced company is doing to "fix 20 on page links per month" ?  It sounds to me like maybe they are link-building for you, but I'm just not sure Regarding the "more than one link per keyword" I am confused by this as well. When you are setting up campaigns, one keyword needs to go to one domain, but in the reports you may find that more than one of your URLs ranks for that term. But, this isn't something you configure in your campaign. What more can you tell us? I'm sure Francisco and I would both be glad to help if we can.

Ranking signals are extremely complex, and On-page SEO is only a fraction of the pie (although sometimes it's a very large piece!) For a broader perspective, run your keyword through Moz's Keyword Analysis Tool - then run a "full" report. This will show you dozens of on-page and external ranking factors for the top ten websites returned for that search query. .... and this still isn't the full story. Questions like this help us learn how Google's search algorithm work, and why some sites rank higher than others, even when we don't expect it. Keep questioning everything!