What does the centershot measure at?
Is the arrow tuned inside (towards the riser)?

My guess is that the bow is tuned too far inside to get a bullet, or you're torquing the bow, but I'll bet the former.
If so, you'll need to change the top hats and move the cam...

 

It's inside the 1/4-13/16 measurement everybody says.

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The top hats keep coming up.... Looks like I may not be able to avoid this, but I want this bow super tuned.

Id take it to a po shop if I felt like the 21 year old behind the counter knew more about bows than I do!

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Yeah...it's not hard to do.

Reset the CS to 13/16 and leave it alone.

Swap the top hats (Jesse Broadwater has a great utube vid about top hats) to get your bullet and bareshaft tune...

 

Apparently this is a Mathews issue. Mine does the same thing.

Rather than just "setting it to 13/16" and forgetting it" hold a straight edge against your riser with an arrow nicked and measure if your arrow is parallel to the straight edge.

http://www.archerytalk.com/vb/showthread.php?t=5294541&highlight=

Good place to start....

 

I would buy a bow press! It's worth every penny if you want it tuned properly.

 

My HTR looks the same. Centershot is where it needs to be shoots fine through paper, etc. Notice how wide that riser is? I wouldn't sweat it too much if the bow is shooting well.

 

How big is your housing and how far is it extended in front of the riser? If the arrow is only 13/16' from the riser, then you're not going to see more than 13/16" on the right side of your pins at full draw if the sight is close to the riser, the farther out the sight is extended, the more you'll be able to see on the right side of the pins (assuming right handed archer)

 

It is pretty normal to have a portion of the sight hidden behind the riser. If your centershot is adjusted to 13/16" I wouldn't worry about it.

 

There are two ways to think about tuning,

1. God himself nails down the powerstroke of the bow and you can not change it and you choose to move the arrow rest left right up down and find the location of the arrow rest to give good arrow flight because it is directly in front of the power stroke.

2. Learn how to move the powerstroke of the bow by yoke tuning or shimming so that you can put it directly behind the arrow rest that you put in a nice central location.

Your bow doesn't have yokes so you could choose to move the cams left or right to move your powerstroke and control your arrow flight.