I think i'm getting this too, though I suspect it is not the playlist but the way MusicBee reads the files on the device.
e.g. I have 859 tracks on the device but if I set the left panel to "Album" I get 699 tracks that are "Empty" i.e. MB thinks there is no Album name. If I inspect the file details under "Edit" in the MB centre window (either with left sidebar selecting "Music" on the device, *or* with the explorer tree set to the file folder itself) the only detail there is the track name. All other fields are blank in MB's Edit dialogue. But if I inspect the track on the device itself (direct on the device) it does have all the track metadata present.
On the tracks that are shown correctly in MB's tree/display panels, these all have the data avalable under MB's "Edit" dialogue.
So it looks to me like MB is not back-reading the track metadata for some files (only), hence it can't organise these tracks, hence it looks like a bunch of albums, artists etc are missing. They aren't actually missing, but MB can't sort them correctly.
Re the idea of transferring playlists as M3U or M3U8, I am already using M3U
Win7 / Android 4.4.2 / MB 3.2.6902
I do find when syncing the last file copy, the playlist itself, does take absolutely ages.