Actually now that you mention it, I did have a similar problem on one particular motherboard. I don't attribute it to linux though so hadn't thought of it. It turned out to be a hardware issue (with the motherboard) though. The card kept resetting due to too low of input power. I had hoped a BIOS update would fix it, but it didn't. I have had a couple of built-in audio modules die and stop being seen by the kernel on old laptops.

Honestly I would just buy a USB interface. I got a Focusrite Scarlett 2i2 and have been very happy with it.