I also have a new pool with an Intellichlor which says my salt is good but my test kit puts the level at 5200. I have read all of the posts about possible inaccurate readings of salt with the test kits. I took my water to have the pool store check it and they got a reading of 4000 with the electronic tester, and my contractor got 4100 with a different electronic tester. My intellichlor diagnostic reads the level at 3500 and has been reading the same value for a week without variance so I think the Intellichlor is unreliable in its reading or out of calibration.
I have a call in to Pentair and will let you know if they ever call back, but I wouldn't trust what the SWG says in light of other tests that say different.