Yeah, he's been saying it ever since the Ives article during the draft. He's also said on the podcast that it is just rumblings, and he has no solid proof. It might be a case of where there is smoke, there is fire, or (especially in Duane's case) it could be just an example of blowing smoke.
In either case, if there is a rift, I would expect Mariner out the door, not Winter. Mariner was brought in to handle MLS trades and the draft, he wasn't brought in for his coaching resume.
The thing that speaks against a rift being serious, is that Mariner turned down the chance to run the whole Revs operation. One would think that if things were really unmanageable in TFC-land, he would have jumped at the chance.