Only the LE and M-powered versions have that problem the full versions of Protools have ADC.
From the PT HD users guide.
'Pro Tools provides automatic Delay Compensation for managing delays from plug-in and hardware inserts, and mixer routing (bussing and sends). With Delay Compensation enabled, Pro Tools maintains phase coherent time alignment between tracks that have plug-ins with differing DSP delays, tracks with different mixing paths, tracks that are split off and recombined within the mixer, and tracks with hardware inserts. To maintain phase coherent time alignment, Delay Compensation should always be enabled during playback and mixing. Delay Compensation should also be used in most recording situations.'
In layman's terms when some plug-ins or external hardware is added into the signal chain of a channel delays can occur between the time the signal enters the item and when it returns to the mix path. This is not the same for every plug-in or piece of hardware and therefore adds varying amounts of delay, in addition those channels with no inserts, either from a plug-in or hardware insert, will have no delay.
What ADC does is correct these delays by calculating the delays and compensating for them automatically. If delays remain in a mix it can affect the phase coherence between tracks. For example imagine you have tracked a drum kit and then afterwards add some compression to toms and compression and reverb to the snare drum. In many cases this will add minor delays to the tom and snare channels so that the other tracks now play ahead, in some cases this will add phase issues.
Pro Tools HD and HD Native have ADC which means that the software makes the corrections to account for this. Pro Tools LE and M Powered do not have this, which means an engineer must first work out the delays induced into tracks through plug-ins and inserts and then make manual adjustments."