Check the ejector rod housing
I guess from your description, it's possible that when your pistol gets hot(ter) from firing the magnum rounds, that this whole housing gets cocked enough that the ejector won't enter the cylinder.
The deal about the cylinder expanding enough to block the rod doesn't wash because (as you said) metal should expand uniformly. If this were so (and it mostly is) then your cylinder would lock up tighter than a drum and not rotate. I believe you said that you had about 1mm of clearance between the rod and the cylinder wall when the pistol was cool. Therefore, I'd think that if it expanded that much, then your 6 thousands of headspace would disappear too. If it didn't, then the cylinder itself might rattle like a bastard on it's pin, as this bore too would expand. Either way, this doesn't sound like the culprit.
Now, if for some reason, the screw that holds the ejector housing were cocked, or if the screw hole on the barrel weren't perfectly lined up, then (as the barrel heats) it might just move your ejector (and housing) enough to cause the interference. I'll bet you a beer that your barrel get's a lot hotter than the cylinder - and would move more because it has less mass at that point.
Next time you fire that puppy with your full boat loads, eyeball the area between the housing and the barrel, and see if you can see a gap. If so, you've found the problem. Fixing it could be as simple as elongating the screw hole on the ejector. Might even be as simple as just tightening that screw. You never know.
But do enlist the help of Ruger. They do have excellent customer service, and they'll track down the problem (and fix it) toot-sweet!
Good Luck!
Unkel Gilbey