The negative of the battery is connected to frame ground. There is no way it can short out to the frame. The positive certainly can short out. The most likey scenario is that the seat or something close to the battery has pinched the heavy cables or other wires.
If a wire is crushed enough, strands can break inside the insulation. You have to inspect any wiring near the seat/battery/frame very carefully. I would guess that the battery cables did not slide out of the way and got pinched when you replaced the seat.
The battery can dump a lot of energy quickly if directly shorted. It can overheat and be damaged internally. It may charge up OK but still not function properly under load.
If the short circuit was present while riding, there is a chance some electrical components have been damaged. You may need a dealer's help to track it down further.
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2011 EC250E
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