Hi, on my cortex, when I plug in an encoder to dgtl3, it works just fine on its own. However, if I have any other sensor on the port dgtl9, my dgtl3 encoder disappears. By disappears, I mean that is simply does not show up in the robotc debugger sensors menu. Take the dgtl9 encoder out and redownload the firmware without it, it appears again. I know as a fact this is not a problem with my code, as I am simply using the pragma sensor configurations, without any actual code. Is this a problem with my cortex?
No, the cortex is fine.
The problem is not dgtl3 and dgtl9 but rather digital ports 4 and 10, the cortex will not support using an encoder on both. One of your encoders needs to be moved. See this for details.