I've had the same problem, and at least on Windows, if you go to Control Panel -> Sound -> Recording (tab) -> HELIX Audio (right click, Properties) -> Advanced (tab), you can change the USB sample rate to 44.1 khz. This is also allowed Skype to use the Helix as an audio input for me. Thanks for the clue on sample rates Smj7!
And an FYI just in case it wasn't already mentioned, the global settings on the Helix itself doesn't affect USB sample rate, you can see that documented here https://helixhelp.com/manuals/helix/global-settings.html.
