Phase invert audio files does not cancel to zero

This post follows on from an earlier post in waveburner discussions.

I have come across a rather strange result, which if someone can shed some light on would be a help.
Logic 8.02
place an audio file on track 1 ( stereo)
place the same audio file on track 2 ( stereo)
put a phase invert plugin on track 2.

bounce through the mixer these 2 files. normalise file. no dither.
Result is not an empty audio file but a very strange and glitchy audio track.
This initially came about through me trying to compare a cdr burn with a bounced cd layout from waveburner ( all the bit rates etc matched).
I get this glitchy audio file with that, so thinking I might have a burner problem, i imported an audio file from a commercial cd in twice, then did the above procedure. That removes the cd burn from being a factor, It then could only be a read issue, i.e randomness between both imports. To rule that out i used just one of the files placed on 2 tracks hence result above, meaning the error is being caused in the bounce process.

Anybody else had this or can tell me what is going on?