For Thunar 0.9.3 (from Xubuntu), when running as root, only the topmost /.Trash trashcan is seen. /usr/local is a different partition, and the /usr/local/.Trash is not shown.
I've just found the following in /var/log/messages: "thunar: Root trash directory /usr/local/.Trash exists, but didn't pass the security checks, can't use it" - so probably this bug should be cancelled. However: what are the security checks that it's looking for?
I've managed to fix this problem by using chmod 777 /usr/local/.Trash chmod +t/usr/local/.Trash though to be honest, I'm not entirely sure what the exact permissions that the system is expecting.