Im surprised to not see anything about this on the forum, at least nothing i could find.

I have an AVIC-X9310BT, and using an SD card for music is a terrible experience for me.

IF i have my music divided into sub folders, it will only show some of the folders.

In addition, not all files within folders are found.

IF i have too many subfolders, it seems to endlessly load.

ie a folder structure like music/band/album/mp3files

IF i put all MP3 files into the root of the SD card, the unit will actually see and play the files, but again not all of them. It will only show between 2000 and 3000 files this way.

Has anyone else had issues like this?

According to the manual the SD card i have is fully compatible, and formatted for FAT32.

I have recently updated to the X940 firmware, so i will see if that changes anything

With my X940BT I had no issues at all. When I bought a X950BH in my latest car I found the same thing as you did but on a thumb drive. I cured most of the issues by using very short directory names and one level from the root, no spaces and only numbers and characters in the names. I had to do the same for many of the MP3 music and video files and generally found they all would work easily. It is a pain to do but now I have the thumb drive pretty loaded to what I want I have about 6 months to get through all of them! 

I have tried the SD card with the new firmware and seems to be running MUCH better!

I have yet to load the card fully and try, but so far several gigs in multiple subfolders loads fairy quickly, and seems to read them all.