So my controller had stopped charging for a while, regardless of what I did to set it up. I sent it off for repair, and recently got it back. The upside is that it seems to be responding to the charging, but the downside is that it doesn't flash orange, it flashes red.
It occasionally will flash orange, but it will only do that for a few minutes when I first connection to a power source, before going red again.
Edit: after a bit more testing, regardless of how long I connect it to a charging source, when I disconnect it, I get a low battery notification, and it quickly disconnects. I am also yet to find anything about the blinking red light.