Although it sounds like this thread has run its course, here's a possibility that (due to impatience) can also cause oblong holes. I've been running into this as I've been drilling longer blanks on my lathe (those for the longer click pens; CEO Executive Clicker, Vertex click, etc.). Since my drill bits are usually not long enough to go all the way through (and also to try and get "clean" entry holes on both ends of the blanks; especially with tru-stone) I turn the blank around and drill from the other end also. Every once in awhile (usually with acrylic, sometimes with tru-stone) the holes are not aligned when they meet somewhere in the middle of the blank. I think there are two things, either of which causes frustration (at the least):
1) the blank may not have been square so when turned around the hole was not centered on the other end in the same place. I usually take care of this when gluing the tube in.
2) when turning the blank around and putting it in the blank-drilling chuck (I use the one from PSI (love it), the blank is a bit "soft" due to the heat from the initial drilling; it is very easy to tighten the blank in the chuck too much and end up with an "oblong" hole at the end you just drilled as the blank was "smushed" a tad. So it isn't enough to just have a "cool bit", you need a cool blank also.