I have noticed the same thing, but i still trust the line over my vision and my putting has been better than ever. (since i changed to trusting the sharpie line) I only use my eyes, at address, to gauge distance not aim. 

Your dominant eye is probably outside the ball when you take your stance. If your eyes are directly over the ball, it should appear straight.  But it could also be retraining your brain after having an open putter face for years. 

I like this answer.

Matt,

Let me start out by saying that I am not that good of a putter.  My main problem is that I don't have a real concept of how hard to strike the putt in order for it to bend what I think is the proper amount.  I used to use the line on the ball and aimed the best I could.  Then as soon as I stood over the ball the line looked off.  I could never get comfortable over the ball, and as we all know, you have to be confident in order to make a good putt.  After a while I just gave up on aiming the line.  I have started doing two things that have helped.  First, I determine which way the putt will break.  Not how much, just which way. Then I take the Titleist name and put it perpendicular to the direction I'm putting. I then place the putter face parallel to the name so that I know that the putt will start out in the proper direction. This gets me pretty close most of the time.  The second thing that I've done is mental.  I stopped being so hard on myself.  I play to have less that two putts per hole. That mean less than 36 putts per round.  I still have an occasional 3-putt but they are getting fewer, and I have more 1 putts than 3 putts.  Last year I averaged 32 putts per round for over 40 rounds.  Now I know that 32 putts is not necessarily good by Tour standards, but for me having less than 2 putts per is just fine.  Hope this helps.  Fairways and greens.

Mark F

Take a piece of paper and draw 2 dots caddie-corner from each other (i.e. top right and bottom left). Place the long side of a credit/debit card or something similar next to one of the dots and and aim the edge of the card at the far dot while standing directly over the paper in your address position. Now, trace a line through the dot along the entire length of the card. Once you have the line started, use a ruler or book so that you can continue the line until it reaches the other end of the paper. Missing left or right will show you how well you aim. Repeat 2 or 3 times to verify your tendencies.

Credit to Dr. Craig L. Farnsworth and his book The Putting Prescription (a must-buy if you want to improve your putting).