If your computer is really old, like from the Windows 98/2000 era, SD card readers were only capable of handling SDHC cards (or those sized up to 32 GB). Not knowing what size is your card and how old your computer is, that's the most likely first guess/explanation.
Another possibility is the computer either missing or has bad drivers for the SD reader, but you will notice this as a problem if you have other cards not showing up correctly in Windows.
Lastly, your card might have errors with the partition table that prevents your computer from recognizing it correctly but not bad enough that your 3DS isn't able to communicate with it.
Depending what you have, try using a USB-to-SD adapter to bypass an old SD reader. https://www.amazon.com/Anker-Portable-Reader-RS-MMC-Micro/dp/B006T9B6R2
There's also try finding a way to back up your entire 3DS stuff from a different computer, reformat the card, and check it for physical problems using h2testw. It's highly recommending you don't skip testing with the h2testw. If the card checks out fine, it's safe to put everything back on and continue using it.
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