My friend had a similar issue and it was all due to how his wiring was ran.
Basically, the ecu harness came in from the engine bay in such a way that moisture would run down it and get INSIDE the MS box, causing it to become erratic, and it had to be reflashed TWICE.
This was easily fixed by putting a "U" in the harness so that the water will drip down on the lowest part of the "U" and not come up to the ECU.
Just something to think about,
Mario