What are you using to get the scancode into LabVIEW? At this point, I don't care which is which. If the scanners are setup as virtual COM ports, then you have to open a specific COM port to talk to/listen to the scanner. If that is the case, then you'll have two loops reading two different COM ports and you'll know from that which scanner provided the code.
If there is some other method of communicating with the scanner, you should still be able to tell where it came from, as you'll call a DLL to check for a scan or something similar.
Do you know how the scanner communicates with the PC (I don't care about LabVIEW at this point)? If you don't, what is the make and model of the scanner?