Are you using the built in scanner wedge or are you using Industrial Browser as the wedge? It sounds like if you can scan into Notepad you are using the built in wedge. If so, make sure that Industrial Browser is not configured to be the scanner wedge as well, otherwise both wedges may interfere with each other.
I've seen similar scanning issues with VM1s and tethered scanners before. Check out these posts for reference:
You may want to also verify that you don't have any custom Scan Handling scripts or Scan Handler settings enabled within the Industrial Browser.