SemAdvance - hmm I don't think so that can be issue. The results of site:
www.whoisdeep.com and site:whoisdeep.com fetch the same amount of pages. Same applies for link: query. The search you did was just to search the strong whoisdeep.com in the pages.
incrediblehelp -
check the results from Live PR checker site here
Can you also tell me what does it show when you run link: query?