2. I think it sorts by track name and I'm guessing your FLAC files have the track number embedded at the start of the track name whereas your mp3's don't? If that's not the case then the track number embedded into the name should be in the format 001, 002, 010, 099, 100... Anyone know the standard convention for track names? When I drag and drop from iTunes it creates the track name as disc number-track number track name
Regarding the order of the directories, I'm quite sure the player simply takes the order in the FAT table which would be the order the directories were copied to the card. Thus changing the directory's date modified or created will not change the order.
There are some programmes that sort the FAT table Sort MP3 files on MP3 Player
I tried using "FAT sorter" to sort my directories and it worked. But YMMV. Always make a back up when messing with the FAT table since you could loose your data.