A flashing CEL indicates a misfire (won't store a code) - if it does it regularly, there could be a problem. Lots of things can contribute to it - water in the gas, bad spark plug, etc. - since it comes and goes, I'd start checking things - easiest thing is probably to start with replacing the plugs. Also - do you always buy gas at the same place? If so, try running a few tanks from another location (I'd stick with a big brand gas) - also, if you have a little water in the tank, you'll want to do something about that (there used to be additives you could use - also, you can try making sure you use the whole tank before filling up a few times)
A misfire can be a very big deal if it continues.