We have resolved the Chult threat and returned to Kuldahar. We have defeated Cedra and all of the Yaun-Ti that attacked us. We searched the rest of the area and end up being attacked but unable to see who is attacking. We can not get to Dragon's Eye. We can not talk to Iselore either. What do we do from here?

What do you mean 'you can't see who is attacking you'? I don't understand this. Are you being attacked by someone invisible?

We can see arrows hitting us and the dialog box tells us that we are being attacked but they are unseen. We have thrown a dispel invisibility spell and thrown fireballs in the area this does nothing. There are no enemies that take damage.

Thats weird.
As soon as you deal with Madae's minions Iselore should thank you. He will remain uncommunicative so long as there is any one alive.
Try switching on your charecters AI. If there are any fiends behind ahut or something which you can't see they (due to a bug or otherwise) they will automatically attack them.

Had you cleared out Kuldahar once before going to Chult?

The AI thing worked. We never did see the creatures on the map, but once they kit one of our characters, they engaged. Still have not gotten Iselore to talk. Searching the map to see if we missed anything else. We thought we had clear Kaldahar before going.