A couple of things...
How many rounds are through the slide and frame in total? Both .40 and 9mm.
Can you take a couple pictures of the 9mm barrel, particularly the feed ramp? Maybe a side by side with the .40 barrel as well?
What is your S&W test fire date or production date for your 40c? There have been small changes to parts such as slide stop assembly, barrels, magazine feed ramp, etc. If you have under 5k rounds through your firearm I doubt any of these things would be an issue but it could be more data to help figure this out.
I do not know an obvious reason that you would have problems with a 9mm barrel in your .40. So, I would closely examine the firearm for any issues.
After gathering all this info I would then start to point at form and if maybe your thumbs are interfering with the slide or slide stop.