There's already been a few threads on strange effects regarding the placement of warp markers via auto-warp in 5.03, reported under various topics
e.g.
http://www.ableton.com/forum/viewtopic.php?t=32642
http://www.ableton.com/forum/viewtopic.php?t=30702
http://www.ableton.com/forum/viewtopic.php?t=28999
it seems, more often with MP3 than with WAV files. I have this effect with both MP3 and WAV files.
I wanted to sum things up in this post: Warp markers are slightly off the beat in 5.03. Auto-warp as such seems to be working fine, and I can use it on old recordings that don't have 100% consistent beat - auto-warp gets the timing right, sets warp markers intelligently, but, it is just slightly off the beat (to the right, "late", that is), when you zoom in.