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the thermal variations on Lithium batteries can cause voltage and amperage spikes and lulls internally and you can't see the issue. Like @gtstorey said, swap to a lead acid battery and see what happens. Has it ONLY happened since you introduced the Lithium battery? I would guess its not a wiring issue, but a power supply issue. If it HAS happened before the new battery, then something that is regulating power is not regulating it correctly.
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