[I realize this is an old post, but my reply may be helpful anyway...]
I had a similar experience with my first 10 batches or so. I would hit my pre-boil gravity, be very pleased, and then miss my OG by a decent amount (too low). I used both a refractometer and a hydrometer on the sample. I measured and confirmed my boil-off rate, plugged numbers into all the online calculators, yet could not explain it.
Turns out the pre-boil wort was not mixed thoroughly enough, and I was actually measuring too high a gravity. My OG was accurate, but my efficiency was not as good as I thought it was on the pre-boil. Now I stir the wort well for a couple of minutes before pulling a gravity sample and commencing the boil. I've also improved efficiency, but that's another story. Bottom line is that my pre-boil gravity measurements are now reliable.