The base station was set to "c", while the working one was set to "b".
It was working again this morning though, I spent an hour and a half in Elite Dangerous with no problems. Nothing was changed since yesterday though, I restarted my computer multiple times, restarted steam, and steam vr multiple times and even reinstalled steam vr and it wasn't working, yet now it is. Again another reason why I think it's some kind of firmware or software issue.
I'm not using the sync cables, since I don't even know what that is, do they come with the headset or something purchased separately? Is it the same as the USB cables?