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Hi Andrew,

Inline with John’s comments;

1. Google webmaster tools is showing links from those sites that are pointing to specific pages on your website

2. Google Analytics is showing “traffic sources”, meaning websites that are sending traffic to your website.

A good link should be sending traffic, but this is not always the case.
Also, a lot of links pointing to your website wont necessarily result in many visits – which is why relevant quality links are important.

Your Google position will fluctuate based on your search habits, device be it laptop, desktop or mobile phone. On your mobile – your physical location will also impact search results shown.

in addition each time you do a Google search the results can come from a different data centre as they have many. This can cause a slight fluctuation if a change is in the wings.

To try and get the cleanest results you can use anonymous browsing. From the top right menu choose “new incognito window” in your chrome browser or “new private window” in your firefox browser.

lastly while webmaster tools is a good start, updates are slow and it doesn’t cover everything.