Open Site Explorer Problems
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I've been checking open site explorer for months now. It doesn't show any changes in the number of root domain links to any of my pages, even though webmaster tools shows a substantial increase in root domain links for each of these urls. Open Site Explorer doesn't seem to be updating. According to Moz, my site is regularly indexed by Moz. But the numbers don't change. I've tested this on a few other sites as well with the same results. How do I get OSE to update the numbers for a particular website?
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Hi there!
I'm so sorry for the inconvenience! We had a bit of trouble with our last Mozscape Index—where OSE gets its information—and decided not to release it. As a result, it's been somewhat longer than usual since the last refresh. As of today, the problem should be solved, and the numbers should be up-to-date.
You can learn more about the issue at the Mozscape blog, here:
http://moz.com/products/api/updates
The most recent two posts deal with this problem.
Let us know if you're still having issues.

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From my experience, there is always a big discrepancy between OSE and WMT.
First, make sure that when you use the OSE, you aren't viewing only follow links or links that have equity. WMT displays all links, regardless of their type.
Next, you might want to check out the "Just Discovered" section of OSE. Even though it is in beta, it should let you know if it is finding any more links at all, as opposed to new domains.
If you are sure that OSE is not finding new links, verify that the links listed in WMT actually do exist and it isn't a problem with WMT.
If they do, and it is a problem with OSE, then I don't know what the problem is. You should consider contacting Moz directly instead of asking on the Q&A.