Couple of possibility's here.
#1: If its been dead for a LONG time, and you setup a static site, Its entirely possible its simply not been crawled. Blogs and such tend to ping themselves when they get setup; but plain-html and some php CMS dont do this. So its worth running it through some ping services if this is the case.
#2: Like Gyuman82 pointed it, the site could have belonged to a blog network. An easy way to answer this, is to pop it into the Waybackmachine and see what content was on there before the last drop. If it was a legit site, your in the clear. If it looks like some low-quality blog, has affilaite links, or obvious blog-network posts, your out of luck.
#3: Pop it into webmaster tools. Sometimes this alone will give you "Archived" notifications of penaltys and stuff. If none of show up, it was not part of a PBN, and pinging it did you no good, hit that manual "Index this page" button in webmaster tools.
#4: Start over with a new site if none of the above helps. Your probably out of luck.
PS: I'm assuming your using original content on this site. The only other thing I can think of would be that your suffering from duplicate content. I would select some random sentences from your content and run Google searches in double quotes..
IE: "Sentence 1. Sentence 2. Sentence 3" and see if any results shows up.