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I had the same problem. The dealer told me that i had a bad "rectifying regulator" (I thought it sounded made up). they replaced it for like $45 and i didn't have that problem anymore. if you have a dealer you can trust ask him about it.

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Q: 1999 Polaris scrambler 400 I ride at night and use headlights I come home with dead battery it has brand new stator. what else could be the problem?
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