So yesterday google webmaster tools has over 5,000 links linking to my site. I get in this morning and now i have 16 links linking to my site and no rankings minus brand terms. I do not believe that I have been penalized but I might have been. After digging further into this it seems that my http://www.domain.com and domain.com are separated and webmaster tools is tracking http://www.domain.com and majority of links are to domain.com. Is this possible or am I wishing to see something that is not there. Any help and recommendations would be absolutely appreciated.