If you add your startup application into /etc/xdg/lxsession/Lubuntu/autostart it will be run automatically twice - its just the way LXDE does stuff.
You can create an equivalent file and folder in your local home folder - this will autostart programs once.
mkdir -p ~/.config/lxsession/Lubuntu
nano autostart
add the text thunderbird into this file and save the file.
As to how to minimize the application on startup - this was recently discussed on ubuntuforums
In summary - install wmctrl
Create a script file called ~/start_thunderbird_hidden.sh
Copy and paste the following contents:
#!/bin/bash
thunderbird &
while [[ $(wmctrl -l | grep Thunderbird) == "" ]]; do sleep 0.1; done
wmctrl -r Thunderbird -b add,hidden
wmctrl -k on
Give this file execute rights:
chmod +x ~/start_thunderbird_hidden.sh
Then, instead of thunderbird in the autostart file above, use /home/[youraccount]/start_thunderbird_hidder.sh