Many of Waves plug-ins carry delay lines that result in audio latency. The track you have Waves plugins on will shift in time and so will lose synch with the other tracks.

Pro-Tools 6.4 features 'Automatic Plug-ins Delay Compensation'.
V5.0 is the first version to supports Pro-Tools 6.4's 'Automatic Plug-ins Delay Compensation'.

If you use an earlier version of Protools and/or earlier version of Waves you would have to manually compensate:

Hold down the command key (Apple key) and click twice on the Volume button of the audio track
that include Waves plug-ins. It will show the delay line in samples.
Select the correspondent audio file and "Nudge" it to the left the exact same amount of samples.