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I don't have a Kymco, so I'm not familiar with the battery box layout, but if you have something shorting out, you would have sparks flying, melted wire insulation, or a blown fuse that would not repair itself as soon as you removed the cover. So that leaves a bad or loose connection at the battery terminals, a bad cable or cable end, or a bad ground where negative attaches to the frame.
When you replaced the battery did you get one with the same dimensions, or larger than the original?
Did you route the battery cables in a different way? Doesn't seem to me that a battery box cover should be coming in contact with the cables, but sounds like yours does, and there is an adjustment needed.
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