So, here's an update. Took my car to the dealer to get it checked out. Final conclusion was that there was no CEL stored in the ECU and they could find nothing wrong with hardware (otherwise stock WRX). So, given the fact that the CEL went away after flashing and no codes were stored, is it possible that the real-time "misfire" CELs were erroneously caused by ECUTEK and were false? Anyone else hear of this problem? I'll be taking it to Vishnu in a few weeks just to make sure.