Using openHAB designer on Windows with openHAB on Linux

I use it this way and it works just fine, So you have the folder mounted correctly on your windows machine? The designer should point to /etc/openhab/configurations/ just to clarify.
My next thought would be permissions, your windows user may not have permissions to read the files in that directory.
This is how my samba share is setup

[openhab] path = /etc/openhab/ available = yes read only = no browseable = yes public = no writeable = yes create mask=0777 directory mask=0777 only guests=no