I am having the same problem. I tried a thumb drive with over 60GB of music and a lot were not shown. I tried another drive with just a few GB on it and all were shown. I think there is a limit on how my GB of music the system can process. I wish I new how many.
Straight from my '15 Tundra owners manual
Items related to standards and limitations are as follows:
• Maximum directory hierarchy: 8 levels
• Maximum number of folders in a device: 3000 (including the root)
• Maximum number of files in a device: 9999
• Maximum number of files per folder: 255
• MP3, WMA and AAC files
I've got mine setup as folders: Group folders with album folders in them. I've heard that organizing them this way is the best way to do it and to not just put the songs on the drive. I'm using a 32 GB FIT and I've heard folks using 60 GB drives with no problems.