that's because when you use you controller you are transmitting MIDI CC data that drives the fader on the Synchron player, while when you manually move the fader on the Synchron player you are sending automation data to Logic. You need to choose to either use MIDI CC or Automation, mixing the 2 is only gonna give you troubles.
And i would also take Andreas advice on not touching the volume, just VelXF and Expression, as Volume is set per instrument by VSL to balance the instruments of the orchestra against each other.
Personally i prefer to map my controller faders to the instrument via smart controls automation, so i can rename my controller faders how i want, and i can take advantage of automation modes, like read,latch,touch,write.
Which gives me the advantage of being able to edit my automation curves live with the controller, rather then having to re-record my fader movement from scratch or edit with the pencil tool.