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This is just a guess. It sounds like the control unit located under the driver's seat got soaked and now works intermittently. A broken immobilizer can affect many systems linked to the car's alarm. Check to see if the carpets are wet. If enough time has passed for them to dry, then remove the seat and lift the carpets to check for mildew etc.
If you do find that water may have pooled under the seat, you'll need to replace the unit or possible have it repaired at a place like Specialized ECU Repair. Also, you should check your drain holes to make sure they aren't clogged which leads to the soaking problem.
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