Also any Android 4.0 non-displayable characters in the folder name will cause it to be 'missing' as it cannot display it.
That is probably why you have random directories missing. Windows will write them in the 1st available empty directory entry - The Android 4.0 that is in the Honda Radio will stop after 4096 entries in the root file system. It read in sequence - Windows reads all the 8.3 first and the long file name second. FAT32 is an 8.3 files system with long names taking up extra file entries.
Android does not read FAT32 USB drives the same way Windows does.