Probably won't help much but the toyota matrix manual lists the following potential trouble areas as cause for P0301
Open or short in engine wire
Connector connection
Vacuum hose connection
PCV hose
Ignition system
Injector
Fuel pressure
Mass air flow meter
Engine coolant temp. sensor
Compression pressure
Valve clearance
Valve timing
ECM
Did this start happening about the time there was any work, service, maintenance or modification done to the car? Not saying it had to be caused by anything, but if the timing coincides, that might be another clue to figuring it out.
You said the CEL blinks at 55, that's usually an indication of an issue that is more serious than one that will just cause the light to come on steady. The manual says
The ECM counts the number of times the engine speed change rate, indicating that misfire has occurred.
And when the misfire rate equals to or exceeds the count indicating that the engine condition has deteriorated,
the MIL lights up.
If the misfire rate is high enough and the driving conditions will cause catalyst to overheating, the MIL blinks
when misfire occurs.