iTunes 12 update
7/16/15: In iTunes 12 sorting by playlist order is the only way to maintain playlist order on iSyncr and in Android playlists. Please use the following workaround below to copy track play order and manually arrange your playlists.

11/14/12: I'm not quite sure why, but we've been seeing an increase in customers who are reporting that their playlists are sometimes sorted in a strange or reverse order after syncing with iSyncr or iSyncr WiFi from their iTunes Library on Windows.

Technically, this is a bug in iTunes that returns the playlist order on Windows, where sometimes when you sort by a Date, Play Count, or Skip Count field, the track order that iTunes reports is incorrect.

We are working on a potential software workaround, but in the meantime, many users have had success fixing this problem in iTunes itself with the following steps:

  • Right-click on the playlist that isn't sorting correctly and choose "Copy to Play Order"
  • Now sort by the "track number", like so:

So if you've been seeing this issue, give that a try. Hopefully it will help =)