You're expecting the wrong thing!!
Not the library's fault
Whether the library produces it properly or not, you're looking for a pattern that rarely actually exists in real-life sounds. Only a perfect sine wave, electronically generated, will cause an even partway discrete appearing 'spike' in the freq. graph. If you don't believe it try firing up a 'spectrum analyzer' visualization in winamp or media player. It's not so much the PC's fault.
Real sound waves are complicated animals
Picture a sawtooth or sqaure wave in your mind's eye. those sharp turnaround - corners or points on the wave, look like tons of higher harmonics to the FFT or even a real fourier. And if you've ever seen a real 'sqaure wave/sawtooth' on a scope, or even a 'sine wave' produced by an instrument that is supposed to produce a sinewave, take a look at all the sharp nooks and crannies in just ONE note (if you don't have a scope just zoom way in on the wave in audacity - the more you zoom, the higher notes you're looking at). Yep, those deviations all count as frequencies.
It's hard to tell the difference between one note and a whole orchestra sometimes in a spectrum analysis.
But I hear single notes!
So how does the ear do it? It considers the entire waveform. Then your lower brain lies to your upper brain about what the input is: one note, not a mess of overtones.
You can't do it as fully, but you can approximate it via 'training.'
Approximation: building some smarts
PLAY the note on the instrument and 'save' the frequency graph. Do this for notes in several frequency ranges, or better yet all notes.
Then interpolate the notes to fill in gaps (by 1/2 or 1/4 steps) by multiplying the saved graphs for that instrument by 2^(1/12) (or 1/24 for 1/4 steps, etc).
Figure out how to store them in a quickly-searchable data structure like a BST or trie. Only it would have to return a 'how close is this' score. It would have to identify the match via proportions of frequencies as well, in case it came in different volumes.
Using the smarts
Next time you're looking for a note from that instrument, just take the 'heard' freq graph and find it in that data structure. You can record several instruments that make different waveforms and search for them too. If there are background sounds or multiple notes, take the closest match. Then if you want to identify other notes, 'subtract' the found frequency pattern from the sampled one, and rinse, lather repeat.
It won't work by your voice...
If you ever tried to tune yourself by singing into a guitar tuner, you'll know that tuners arent that clever. Of course some instruments (voice esp) really float around the pitch and generate an ever-evolving waveform (even without somebody singing).
What are you trying to accomplish?
You would not have to totally get this fancy for a 'simple' tuner app, but if you're not making just another tuner app them I'm guessing you actually want to identify notes (e.g., maybe you want to autogenerate midi files from songs on the radio ;-)
Good luck. I hope you find a library that does all this junk instead of having to roll your own.
Edit 2017
Note this webpage: http://www.feilding.net/sfuad/musi3012-01/html/lectures/015_instruments_II.htm
Well down the page, there are spectrum analyses of various organ pipes. There are many, many overtones. These are possible to detect - with enough work - if you 'train' your app with them first (just like telling a kid, 'this is what a clarinet sounds like...')
