You could try one more thing, just to see if the whole rebuffering seems to function as it should: Change your audio buffer size. This should not have any effect on the position of the data[0] = 0.0 samples.
Are you resetting your queues in Reset() (i.e. clear input, reset output to FFT_BUFFER_SIZE zeros)? I ask because if you don't, then your plug-in will start processing right after it has been added to the track. This is not a problem per se, but then it will be very hard to predict exactly where the data[0] = 0.0 samples will go. Note that if you do Reset() then the queues will be reset at playback start, but still not necessarily at the beginning of the audio item.
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