Why Post Indexer can't find all my articles?

I have a relative big network (3000+ posts) and I had no problem indexing the smallest blog of my network but for the main site (the one with more than 2000 articles) this plugin is running for days but at the end it did not find anything, not even a single post is added...

Hoe am I supposed to solve this problem? I have tried a coupple of times already but nothings change.