The latest update to the 3DS firmware is listed by Nintendo as a "stability" patch.
http://www.nintendoworldreport.com/news/26847
Nintendo has released an update to the 3DS firmware that, among other "stability" fixes, corrects the Ridge Racer 3D freezing bug that they introduced in the eShop update last Monday.The newest version, 2.1.0, also includes unspecified "minor adjustments to enhance user experience."
3DS systems set up to prompt for updates automatically will be notified via a SpotPass alert. If the 3DS is not setup for these alerts the update option is available in the 3DS system settings menu.
SpotPass doesn't just notify you of the system update -- it pre-downloads it so that you can install it as soon as you open the system, even if you are no longer online. This should help Nintendo deliver firmware to people who don't have regular home access to WiFi.
The only thing i can think of is that I had Zelda (GBC) on hold. I didn't think this would affect anything though.
It seems like they're following the PSP style of updating. My system had downloaded the update, but my battery was very low. I plugged it in, but it said that it would not update until the charge level was higher and would start automatically once the desired level was reached, which it did.