The keyword in this question is rain...
Water and the engine electrical system just do not 'mix'.
A few pieces of the puzzle to start...
An ignition misfire has been detected
normally the coil pack
This happens when there is an Active Misfire, or a urgent pending service matter. Get your codes checked.
A flashing check engine light usually indicates a misfire. You need to check codes to know possible causes.
I believe it is blinking because there is a misfire inside the engine. Meaning that the timing is off. This could be because the timing belt may be old and the teeth are chewed and are not as rigid. That was the case for my 96 tacoma.
What causes misfire 302, 304 and 306
Misfire detection.
the gun powder ispacked to tightly and the preassure builds up and can cause it to misfire
In general (very loosely) a misfire can be a bad plug, wire or coil.
Time to replace seals, this usually causes misfire.
Mercury.
A misfire will cause flames to come out of the carburettor