I did a quick test with Pyglet, and it suffers from the same problem. I
take that to mean that using sdl event callbacks does not work around
this problem.
What that suggests to me is that the problem lies with the way the USB barcode scanner interacts with system components, well below the application layer. So like maybe with the HID driver or windowing system of your computer.
I'd try it on a different platform, to confirm.
... and as far as workarounds go, maybe you can build this into the game design? Like make gameplay be about how digits change? or the number of distinct digits found? something like that...