Only one COM port is coming from Digirig and that’s the one that disappears when you unplug it.
Sounds like it’s COM5 in your case. Use it in your digital modes software configuration.
COM3 must be coming from some other equipment connected to your computer. E.g. my ICOM IC-7300 also uses the same UART Bridge so there’s a Device Manager entry that walks, talks and acts like Digirig but not quite Digirig.