I haven't had time to research and find out if this has already been reported, so hopefully I don't make myself look like an idiot.
In the main Samba config file using the following code:
include = /etc/samba/%U
with a file existing correctly will cause Samba to not recognize the additional included file. Initially it looks like it worked, however when you attempt to go into those shares contained within the /etc/samba/jane file Windows comes back with inaccessible, then log file says "couldn't find service *". However, if you place a ".conf" at the end of the line (or anything else) like so:
include = /etc/samba/%U.conf
it will function as expected. This took me months to figure out why it wasn't working properly. :(
Tested and this works in latest 3.2.x codebase.