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I got this reply from help@seomoz.org:

Your request (#41376) has been answered! See the comment history below. If you're not quite done with this ticket yet and want to add a comment, please reply to this email and the ticket will open back up.

If you wrote us using an SEOmoz account email, you can also view your ticket here: http://seomoz.zendesk.com/tickets/41376

Aaron Wheeler, Oct-27 14:03 (PDT):

Hey Tom,

Thanks for reaching out about this, and I'm sorry you're not seeing your links in OSE. It sounds pretty frustrating, and totally understandably so. As you know, we have made some updates to our crawling for Linkscape - sadly, with a few hiccups. This is the first quarte including the new metrics, which is why you're suddenly seeing the changes. Our new crawler is built to be fresher, but it is going deeper into domains, and, unfortunately, not visiting as many domains. This is probably why links from those domains aren't getting indexed. Domains with a high mozRank are getting crawled deeper, but domains with middle to lower mozRanks are not getting crawled. Our top priority now is to get the domain diversity back up to or better than that of our last quarter updates (as was originally designed) so that we should have many more inbound links. If you're interested, here's a link to the blog post about the update's metrics (it sounds like you may have read this): http://www.seomoz.org/q/link-analysis (scroll down to Kate's answer).

Also, just to be completely transparent about the update, you may see “questionable” links with weird file extensions - this is due to the crawler reaching much deeper into sites where there are more download links. We are looking into fixing this bug as soon as we can so these won’t be counted as links.

I hope this helps explain the changes. We are so sorry about the inconvenience and are focusing our efforts right now on getting this fixed! I wish there was more I could do for you personally, but at the moment, it's a matter of waiting for the index to expand. I've closed this ticket for now, but please let me know if you have any questions or if there's anything else I can do to help and the ticket will open right back up.

Have a great day,
Aaron

--
Aaron Wheeler
SEOmoz Help Team
http://www.seomoz.org/team/aaron

These top links that were found in OSE before had been found for over a year after every crawl. Since July they have disappeared. I don't know why it wouldn't crawl Business.com.

Keri,

I know I have to change the content on a lot of the city pages. There are so many that I hadn't got around to them all. Creating new content for all those cities isn't easy.

Partners.html and Gotlinks.php are my links pages. Don't have much control on Gotlinks. Partners creates a 2nd page once it reaches more than 15 links and the title is then duplicated which I have no control. /lose_weight_fast I created myself which I do control to give myself links.

I see what you mean about keyword stuffing the URL's of the city pages but so far it has helped in Google except for Arlington_Virginia so I will probably shorten some of these and add it in my .htaccess file.

As far as the /blog well, all I get in my comments are spam so I did okay a few of these to let Google see some bloggers were interested in my site.

Thanks for pointing all these out. I will take care of most of it but the third party links mangers are a bit more challenging.

Almost 2 months later from last post (Sep 5) here and I am wondering why this problem with OSE is not rectified??? Oh yea, here's another $100. Thanks so much!!?

Okay, my website is www.astrobrite.net . Why did OSE find the following top links on and before 5/19/11 but now it doesn't list them even though they are still linking to me???

http://www.lakerealty.com , http://www.business.com/ , http://twitter.com/Astrobrite , http://www.webring.org/cgi-bin/webring?ring=novamembers;id=32;skip , http://www.house-cleaning-services.com/house_cleaning_VA.htm , http://www.weddingplanningdirectory.com/reciprocal.html

That is just a handful. There are more that it is not listing. My "Page auth" went from 62 to 57 and "Domain auth" went from 55 to 49. I had 6,008 Total links and now OSE shows 4,565.

If you are going to say OSE is not crawling right, why doesn't it remember the top links from before and check to see if they are still linking?

In previous months ago open site explorer listed many other sites linking to mine. I have checked those sites and they are still linking to my site. Why doesn't open site explorer list them?