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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.