Posting this here in case anyone else has issues like this.

I tried all the usual Mac suspects: reset the PRAM and SMC. Clear caches. Then reinstalled the OS. The problem continued to happen. I discovered that often, a good solid SMACK or pressing alternatively on each side of the trackpad really hard would restore functionality for a limited time.

But the problem always returned. This would seem to indicate a hardware problem. Ended up taking it to the Genius Bar at my local Apple Store.

While the problem couldn't be reproduced at the store (typically), they agreed to replace the trackpad which, on the Retina Macbook Pro, involves replacing the entire upper part of the case. Thankfully, my Mac was still under warranty.

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