Rob has made a couple of very good points about the glue. If it's not the mfgr. recommended glue or, if it is, and it's not applied to 100% of the boards, you may get squeeking. Assuming your subfloor is as sound as you say, it's possible that the seams of where the cork meets may be causing the squeaks. If you can remember where the seams are, you may have a clue. If you have some of that cork, put 2 pieces together and apply some friction. You may 'hear' the same sound.
You'll have to check with Pergo to see if their warranty allows the cork under the Pergo. Call them or e-mail them Pergo WEB Page. You may want to find out the make, model, and serial number of the cork first because it may prove useful to the folks at Pergo. Tell them the order that you posted as to what 'layers' are where. Also tell them the joist spacing (16" OC or 14" OC or 12" OC), etc., etc.. My best to ya and hope this helps. If you find out what's up, post a follow-up attached to your original post and we'll all learn!