My best guess is that the cube plastic contacting with the intake is generating a large amount of static electricity, causing the port failures. I have heard a lot of arguments claiming that metal shavings are shorting the brain, but our investigation into the failures didn’t lead to this conclusion. Our teams investigation and repair can be read at this post. In summary, the RS-485 tranciever chip is weak to static electricity. Friction between components builds static in the motor which travels down the wire to this chip in the brain, breaking it.
I would suggest doing what @marinmersenne suggested. If the intake is floating on plastic bearings or other joints, try to find a way to connect it to the metal contacting the brain.
Unfortunately, unless Vex decides to reinforce the smart ports with static protection, we may have to live with this. I have detailed a repair process for the brain ports for those out of warranty. It technically makes it unusable for competition due to modification restrictions, however the repair does not affect performance and is using the exact chip the original brain uses.