Sorry to have taken so long to reply to this -- this is the sort of question that makes me really want to go back and review the behaviour of the program carefully, and take a look at the source code, and I'm afraid I haven't had time during the last month to do any of that having been somewhat swamped with other things.
In a 1024-point spectrogram with zero overlap, you should find that column N that is aligned with samples N*1024 to (N+1)*1024-1 in the audio waveform contains the data calculated from samples N*1024 and (N+1)*1024.
With overlap, the intention is to centre the displayed column on the centre sample of the source frame. That is, given a 1024-point spectrogram with 50% overlap, the column N aligned with samples N*512 to (N+1)*512-1 should contain the data calculated from samples (N*512)-256 to (N+1)*512+255.
Chris