Okay, now I get it...
Since I use the script below to run btsync as a service on my RasPi, I did not relate the 'current directory' thing. So, when I call the script manually, BTSync creates the .sync directory within the current Working Directory... So, at boot time that is the Root, but when manually entered '/etc/init.d/btsync start' you have to be careful where to enter the command.
#!/bin/sh
# /etc/init.d/btsync
#
# Carry out specific functions when asked to by the system
case "$1" in
start)
/<btsyncpath>/btsync
;;
stop)
killall btsync
;;
*)
echo "Usage: /etc/init.d/btsync {start|stop}"
exit 1
;;
esac
exit 0