Yep. Retarding the ignition timing at partial throttle would do that.

Yeah, but it was doing it on the stock PCM as well. It isn't anything new since the introduction of the Intense Standard. I didn't quite take the time to understand the theory, but does it still apply in light of this information?

Yeah whether or not you have the I pcm or stock, your computer thinks some % of exhaust gas is being sucked in during partial throttle. Exhaust gas lowers combustion temps since it displaces air. This also allows for more timing. But without the exhuast gas the timing is too advanced. And your increased compression ratio also raises combustion temps. So the two together may be giving you your condition.
So assuming you don't have a vac leak, you may want to back the timing down at partial throttle.

Gotcha. So basically I need my custom tune sooner rather than later.

I'm running a bit richer in the midrange than I was before, but the knock is still there. Wouldn't a rich condition help fight knock? It doesn't seem to have gone away any more than when it was running leaner.