Something as serious as a misfire can also cause the check engine light to flash.

Why yes, I did once lose a whole-ass cylinder in a 4-cylinder, manual transmission car. While a couple hours from home! It broke a freaking exhaust valve while we were just cruising along, and the light started flashing immediately with a code for cylinder X misfire.

Funny enough, other than the loss of power it drove alright while in motion, including on the highway. It would immediately stall if left to idle at a stop light, though. I think I ended up using the hand brake to hold still while keeping my foot on the gas to keep the revs up. Fun.