'01 Legacy - ignition problem?

When the check engine light is blinking, it indicates a possible ' catalyst damaging condition'.. basically the engine is misfiring/ running so rich it is dumping raw fuel into the exhaust tract, where it will damage the catalytic converters. The fact that the problem occurs mainly on rainy/ wet/ humid days further reinforces the possibility of an ignition fault/ misfire. When there is a lot of moisture present in the air, a weak ignition path ( high resistance from wires or a large spark plug gap) will cause the spark that would normally ignite the fuel/ air mix in the cylinder to seek another, shorter path to ground (water conducts electricity). A simple tune up could rectify the problem.. Worst case scenario, you could have a faulty ignition coil or crank position sensor.

Maybe the car is just at a mileage when cold starts are not as efficiently controlled by the engine computer (normal engine wear) or maybe you have clogged fuel injectors. On most cars with a check engine light, the light comes on or flashes during the first 30 seconds or so of startup indicating that the ECU is going through its startup diagnostics (checking for problems) this is normal. If the light comes on and stays on thats when we have a problem that needs to be addressed. If during normal driving the check engine light comes on but eventually goes out on its own- that is an intermittent problem and that is not much to worry about.

if it goes away I'm guessing it's either the spark plugs are going and need a few seconds to really heat up or there is some moisture built up on the MAP sensor and goes away when it warms up and drys. If it's been really cold there may be moisture getting into the fuel lines around the fuel rails or injectors too.