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In the control box the shifting part had detents to hold the cables in neutral. When you use the warm up lever it is supposed to be independent of the shifting mechanism. What happens is after a long period of time the parts break or wear and the detent no longer holds.
Parts are not available for the older control boxes like yours so there is no repairing it.
What I would recommend is getting a new control from Yamaha, not an aftermarket control. If finances are a concern they do show up regularly on auction sites such as e-bay.
If your key switch is external to the control then it is an easy swap. If the key switch is in the box then you want to get a control with the wiring harness. Yours should have a 7 pin harness. Disconnect it back at the motor and count the number of pins then simply get a box with the wiring harness with the correct number of pins, which will be almost all the older boxes.
This should do you.
Please post back with any additional questions on this. Thanks.