Hey Matt,
The flashing CEL does indicate knock with the SC setup. That's why no DTC codes were stored. You were getting knock. I ran into the same thing before with the SC setup. It would happen if I downshifting, was heavy on the throttle, and then all of a sudden let go. This seems to cause knock. I think this is because you have a lot of load on the engine, manifold pressure is built up in the manifold, and then all of a sudden you let off but the pressure is still there.
Not sure if that's the exact cause but I noticed it would only occur if I was at high RPMs and a had heavy load on the engine and suddenly let off the gas. I learned to let off the gas more progressively. Am I'm not sure if the ECU eventually learned because I didn't run into that issue in the last year or two. So anyway, this isn't a show stopper. Just try to transition more smoothly off the throttle if you're in a similar situation. I eventually learned to not get the engine reved up like unless I was for sure ready to go. Just get over and wait an extra second before getting on it, you'll be leaving those cars in your rear view anyway

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K-E-N-N-Y
04 TSX CGP 5AT Auto - 265hp / 199tq
Hondata K-Pro / CT-E Supercharger 8 psi
Advan Kruezer Series X...a few more mods here and there