Okay, so it's not really the A/C, but really S-Mode.
Half the time I have trouble getting smooth engagements in any gear, and I notice the RPMs drop quick then S-Mode tries to rev match at some awkward moment. I turn it off, and the RPMs drop slower so I'm able to get smooth engagements. Downshifting with S-Mode active doesn't seem to give me any problems.
It's just weird why the RPMs drop so quickly and rev match a bit out of sync. Basically I purposefully depress the clutch pedal, shift into gear, and let the engine rev down. It'll rev down quick, then the throttle blips slightly.
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