First thing you do is, remove the bolt that holds the battery ground strap. Then clean and shine the area and the strap end before reinstalling. My guess, is that your ground is bad on your battery and does NOT provide current to your ignition system when you remove the jumper cables. The 6 volt system requires a good ground and heavy battery cables not the skinny 12 volt ones. You can check the ground connection by hooking the jumper cable from the tractor battery to a good ground.
The control box has a resister on the light switch that is a manual control for the charging rate. This box has a fastening screw that must be in place for the resister to have a ground and operate properly. If you have a voltage regulator instead of a cutout relay, then the manual resister control is not needed. There are 6 volt wiring diagrams on my web page. Duey