"I've entered my league scoring on the Leaguesync page and I'm wondering why when I run the Value Based Rankings that it has a handful of kickers, tight ends and defenses in the top 50 players on my x-factor sheet? There is no way I would draft a defense, kicker or TE within the first 50 selections. Also after 50 positions or so, the x-value goes negative. Why?"

The report is not necessarily saying who to draft first. Value Based Rankings are not necessarily a drafting order list. 

Value Based Rankings shows the most valuable starters based on your inputs. The key word here is starters. 

So, lets say your league has 14 teams and you guys start 2-RBs each. If that's the case, the 29th RB has little value as a "starter" (but sure he's more important than many kickers). 

Finally, if you want Value Based Rankings to rank more RBs early, just add 1.0 or 1.5 to the RB starter requirement and that will do it for you.

For more information, read: "How do I use the Value Based Rankings for drafting purposes"