Does "Main program window" refer to the Settings window? That's what your description sounds like. So, manually (no card reader) pressing a hotkey works with the clock window open but NOT if the Settings window is open. Is that right?
Is, that's right, but now I tried with some keys like H, G, and they work, so I guess it's like you said, some work some don't.
Now, as far as why the TD doesn't detect the reader pressing the "B" key I honestly cannot say. The TD has only one way to detect hotkeys, so if the reader simulating a keypress doesn't trigger anything in the TD, there's little I can do about it unfortunately.
Which is the only way? When running the card reader program with notepad, if I run a card through the reader, it automatically type the desired hotkey written in the program.
So if I set F1 to be the key pressed, t writes "F1" on the notepad.
Out of curiosity, what happens when you run a card through the reader while an input field in the TD has focus? For example, click on the Notes or Description field on the Game tab and run your card through. Do you see the "correct" input as you did in Notepad?
If I run the reader with TD's input field open, it writes the key inserted in the card reader program.