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 www.domain.com and domain.com are separated and webmaster tools is tracking 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.