Put the game in switch edge test mode and spin it to see if the switch gets activated. You may have a bad switch, a broken wire or electrical problem, or it may be just a matter of bending the switch arm so that when the spinner arm moves down it actuates the switch. Pull the playfield up and check those issues first and then report back with your findings. Hopefully you just need to adjust it.

The game will give a message when you power it on if a switch hasn't been activated in 20 or 30 games, something like that. It should stop when the switch gets activated.

Mounted on the coin door there should be three buttons that are used to go through the menus. On System 11 machines I think it is the middle one that you can push in and it will stay in, and push it again and it will pop out. Depending on what position it's in the menu will cycle forward through the selections when you push the third button, or backwards. Also depending on if it's pushed in or out when you push the first button, the menu will go into the tests and adjustment menus or audits. It should be covered in the manual. Once you put it in switch edge mode you can hit individual switches and if they are working correctly they'll show up on the display.

The software is telling you "hey the scoring switch on the spinner hasnt been closed in a while, it needs fixed".

well done.
My PIN*BOT will give me an alert if the 100,000 switch hasn't been hit in a few games. The early system 11 games will do this, just as a check, which is cool, but sometimes annoying.