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Thanks for the answers. Haven't had those figures earlier but I guess you are right. Didn't handle them correctly. I guess it was a mistake from my part. Thanks again.

Yes i bhlieve it will and since google follows javascript, it should be seen as a link

I was hoping for some more input regarding this. I appreciate your input David and will change the meta-robots around a bit. But thought I would get some more input, perhaps someone that wanted the categories to be index, follow as I have heard somewhere else.

Perhaps you are right about the links but it feels strange that we have dropped that far down in that case. We have around PA 57 and DA 48 with almost 250 root domains linking which is quite high comparing to the competitors. Even though some of the links got devaluated, we shouldn't drop 100-200 places for many of our more difficult keywords. I will continue working with the links, and go through the onpage seo to see if I can turn things around. Would be sad to let the site go.