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I am currently having the same issue as my domain authority is different on both of the campaign views.

Thank You! The site in question had the same malicious scripts detailed here. After finding them and removing them the site is up and running as it should thanks again for the advice.

Thank you very much for the links you provided. After doing some research I found some shady scripts on the website templates after removing the scripts everything seemed to work fine. We have changed the login info because unfortunately it looks as if the designer himself inserted the malicious code. Again thanks for the links and the info they got me on the right track.

Below is the malicious script for anyone having similar issues

*Update 9/19/2013

So I finally have more details the site is a joomla site and is hosted on godaddy. The weird thing is the malware message only appears when browsing the site in chrome it comes up fine in internet explorer any specific reason why that would be? Also we noticed that on the joomla template there were about 6 scripts after the tag that were adult site related and have nothing to do with our site, any ideas? I appreciate all/any suggestions and or advice. Thank You.

I had a client recently pay about $300 for a site design that she hosted on go daddy. This is the site www.shirianfabric.com can anyone tell me why this would happen its only been live for about three months and out of no where we get this message? My client is thinking maybe the designer inserted some kind of malicious code?as he is now charging a couple hundred to fix the issue. Is there any way to look further into this? Im not sure a webmasters account was ever set up for this site so any advice would be greatly appreciated. Thanks.

Thank You for the further explanation, since i posted my question things have definatley updated to reflect many of the most recent links we have created. But for some time there it did seem as if everything was frozen only the same links would appear and after posting my question even my domain authority jumped 3 points over night. Thanks again as it looks like my campaign stats are back on track.

Thank You Keri, I do not know what was wrong but it has been fixed. I see all of my information in the campaign and my domain authority even went up three points. Thanks Again.

I am looking at my campaign competitive link analysis and the content under the (followed backlinks, linking root domain, top pages, and anchor text) tabs is different than the information when I open up opensite explorer do you know why?is that normal?