What works for me is the (pressure) of the flick, try a lighter pressure with your finger when needing to scroll short distance. Stronger pressure with finger for a longer flick.
There are already topics on this. Every time you "flick" the page to scroll, it'll scroll faster. This is an intended feature, as it helps when scrolling to the end of a long document. All scrollable elements in the iPad UI have this feature.
How long have you had your iPad? I had similar experiences for the first day or so, but I have subconsciously adjusted after using it for a bit. I love the responsiveness of the screen.