We have a Roborio that seems to have dead usb ports. We had to download firmware over ethernet, and our USB camera doesn’t register. They were working before summer, then weren’t afterwards. Everything else seems okay. Any ideas? Is this possibly something that was disabled in software? Has anyone else seen this?
I recommend you contact NI. I seriously doubt there is a software problem if you already re-flashed the RIO.
What’s the chance metal shavings are sitting in the ports?
EDIT: Before opening the rio, just vacuum out each port (spi, analog, usb, pwm etc.) as JR0405 said.
What color is your power light? I’m going to bet its red, and you have a short on the 5v rail somewhere. I’d take everything off the rio so it is bare and try again. If the issue persists, you likely have to open the rio. Once it’s open, used a vacuum to GENTLY remove the debris. You can use compressed air instead, just be mindful not to get anything in your eyes.
When putting it back together, align the small raised rectangle on the back bezel with the pins for the MXP port.
If your power light is green (and doesn’t go red after a few seconds), I’d probably reimage the rio. Not sure if you meant reimage when you said firmware, as they are slightly different. If you did reimage, and your power is green, I’d verify that the camera works on another rio or a computer. If that comes clean I’d think an email to NI would be in order.
DO NOT OPEN YOUR RIO. NI may void the warranty and refuse to help you if you open up the RIO. There is an old post by Marshall about voiding the RIO warranty which I can dig up later.
Try the vacuuming and then just email NI and ask for help.
Here in the warranty info. While you can call it an unauthorized maintenance, the warranty is only good for a year from your date of purchase. If you are still in the warranty window, sure give them a call. A vast majority of teams are not in that window anymore. Considering OP is a 2016 team, their warranty likely expired January 2017.
In CSA training, we have been told to open rios when appropriate to remove shorts. Often a vacuum to the exposed ports is enough.
I’ve had folks from NI tell me to do that, and then they warrantied it afterwards. It’s really not a huge deal.
Also, what Garrett said.
The difference is mostly in the order of what happens. If NI tells you to open it up or FIRST tells you to open it up then you’re in the clear.
Please don’t make me try CD’s image search function
We first noticed our USB ports dying at an offseason event. They had worked the night before but when we went to our first match it all went down hill. First the USB ports stopped working and then slowly the talons stopped receiving power. We ended up scrapping the rio and it works fine. An FTA and other teams confirmed it is hardware not software. 
Definitely call AndyMark and NI. Don’t assume they won’t honor the warranty–NI really bends over backwards to support FRC teams. I’ve never had a better RMA experience than with them.
I reported the same problem as the OP (dead USB ports) on a Monday and had a replacement roboRio in our bot by that Wednesday evening. We sent the old one back the following week.
Agreed, even outside FRC, NI provides great support - on the phone and presumably in person. The website, not so much – CALL.