The cruise control light flashes when the check engine light is on.

Definitely take it back to the dealer and make use of your warranty. It doesn't sound like it's anything tune related. PIGSTi makes a good point so I'd be mentioning the possible Brant keypad issue to them as it's a fairly common problem with similar symptoms.

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MY99 WRX (Sold)
MY06 WRX 241hp 430nm atw (Sold)
MY09 BMW 135i 247kw atw (Current)