I won't be much help to you here but this week I updated MB to 3.3.6962 from an older version (3.3 but can't remember the rest of the version number, but it was a couple of months old). Since the update when I sync my iPod Classic the ratings do not change on MusicBee if they've been changed while listening to my device.
This is definitely a new problem because I alter ratings regularly and sync regularly and it's been working previously without flaw, and now it never works.
There is no issue with ratings updating on the device when changed on MB - only vice versa.