First, I don't know what you mean when you say that the scan rate isn't what you select. That doesn't sound right. You should look into that.
Second of all, if you are reading in a signal that you generate 1500 Hertz, you need to acquire the signal at a significantly higher rate that you generate it at in order to avoid nyquist frequency problems. I don't remember everything well enough to tell you exactly what frequency to scan at, but I think you would be safe with about 150kHz would be more than adequate.
As for your FFT, once you get the proper scan rate, you should be okay with your FFT. However; if it isn't you will have to figure out the exact error, and then add the shift back into your results. For example, if your scan rate is +1%, just s
ubract 0.01 from your results (I think...)