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Do you know what code is causing the check engine light to come on?
Ok, here's the thing.
First, when the check engine light comes on, the cruise control is disabled. This is why your cruise light is flashing, Subaru has that as a safety in case the engine light has something to do with the electronic throttle.
Second, when the check engine light is on, there is a code. This is what is making the light come on. Once you know what the code is, you can then locate the problem and resolve it. Once it is resolved, then the lights will stay out.
There are over 500 reasons for the check engine light to come on. This is why we need the P code that is causing it. This will not go away until the cause is resolved. If the light is going out on it's own, then it has to be scanned when the light is on. It has to be something the car is testing as it goes and either passes at times or is reset until it's tested again.
Flashing check engine light usually means that there is a cylinder misfire. Typically the ignition coil or spark plug wires are the root cause of the problem.