Yeap, so far if I go to the home screen before synchronizing an ereader it will work just fine. It should be the same if I do the sync from within a book which is only on one of the devices.
Clearly my mistake was to prompt the sync from a book and keep it open, since I had to open (and put a newer time stamp) that book again to sync towards this device later.
To sum up, by synchronizing from the home screen only, it works all the time
