I've been getting this issue this evening, and it is the first time it has ever happened to me.
I started one RS3 instance on my laptop at 7:00pm local time, and prior to that had no instances running for ~16 hours.
At 8:00pm I tried to start my second instance on my desktop computer (with the first RS3 instance still running) and got hit with the error.
Closed Runemate, restarted computer, re-opened Runemate and Runescape multiple times and still could not run a second instance.
It has now been a little under an hour and I still cannot run the second instance.
The only interesting thing I noted was prior to loading Runemate on my desktop, I had to update Runemate.
Unsure if this has anything to do with how instances are recorded, however thought I would mention it regardless.
Still getting this issue 24 hours later.