This is due to the immense amount of processing needed to run these particular plugins, coupled with the lack of plugin delay compensation in Pro Tools LE. A complete chart of plugin latencies can be found here: www.wavesupport.net
To align the processed tracks with the rest of the session, you can move the tracks with plugins forward in time so the processed audio aligns with the remaining tracks. Alternatively, you can move the unprocessed files back in time.