I have that problem VERY often with the stock putter. I play STA a lot, and the greens are crazy and fast. However, I will often get a round where I can aim as far left on the screen as possible, hit it "excellent", and it comes off the putter right of the hole already!
It's very frustrating, but not much I can do. I believe this is what the game-makers refer to as some range of variability or something. They have coded into the game a range of acceptable outcomes for a given shot. So, even if you hit it perfect, it still might not go where you expect it to. Conversely, the theory is that you could mishit it and it could end up better than expected. However, I have noticed the range of this variability is WAY higher with the stock putter compared to the purchased ones.
Personally, I think that's their way of trying to force people to buy clubs in order to have a more consistent experience, which is pretty frustrating!