As I am sure you know, Pergo and other similar systems are 'floating' floors. These floors are attached to each other with glue and not attached to the floor in any way. Cork should not cause squeaks and if it is happening in only a couple places I would guess two different causes. First... as well as your subfloor might be secured, it may be the cause of the 'couple' squeaks you mentioned. Second... floating floor systems like yours require a top notch glue job when installed so the floor 'floats' as a single mass. If special attention was not made in applying the glue to 100% of each seam length then a few loose tongue-groove sections of seam might be causing your squeaks. Try to identify the squeaky places and closely inspect the seams in that location.