The tradeoff on a FFT is time vs frequency. So you can have either accurate time data or accurate frequency information. If two notes cross a time window you're going to get the note in between. But if you shrink the time, then you don't get enough frequency resolution. Because pitch is logarithmic (the difference between C1 and D1 is less than 2Hz; C4 and D4 is 32Hz) FFTs really don't work that well for this sort of stuff. Short, low notes in particular are a killer. And the loss of bucket resolution down low makes detection of the fundamental very difficult. The big bump in the wigglegrams that tool provides are not particularly useful for the specific task at hand.