Are you experiencing a particular problem with your EBD? Buying new boards at random is a pretty expensive thing to do if you don't need them.

That might be one problem.

Some of the header pins are removed, it helps identify where and which direction to plug a connector in. So his might be normal. Which pin is it, on which board? You can find schematics for your game at ipdb.org and there will be a picture of the board in there somewhere with connector names like J1, J2, etc.

Or, it's possible that you do have a broken pin, and that pin is for the trough switch, in which case you can save yourself a few hundred bucks by just getting a soldering iron, a solder sucker to remove old solder, and a rail of header pins for a few cents.

And if you have no interest in DIY, and would rather just spend the $ and swap boards, that's cool too. But it's definitely in your interest to identify the exact problem first before doing that, and make sure that swapping boards will fix it.