Well I figured it out,

Its kind of hackish, I wish I could have found a better way but this way works for now.
I am running Xubuntu 13.10 and Mozilla Thunderbird 24.2.0.

What I wanted was for a notification bubble to pop up when I got a new e-mail.

What I did was installed the extention "Fire Tray 0.4.8" in Thunderbird, which showed a Thunderbird icon in the notification area plugin in my panel. Then if you right click the icon and go into the preferences option there is an empty field that says "Launch on count change".

I wrote this python script and "chmod +x"'d it:

#! /usr/bin/python



"""

    This program is meant to be launched when

    a new message is detected by the mozilla

    thunderbird extention "fire tray"

"""



import pynotify

import sys

import getopt



# full path to the icon to be displayed in the notification bubble

ICONPATH = '/usr/share/icons/numix-icon-theme-circle/Numix-Circle/48x48/applications/thunderbird.svg'



# Time out is in seconds

TIMEOUT = 45





def sendmessage(title, message):

    pynotify.init("Mail Notify")

    notice = pynotify.Notification(title, message, ICONPATH)

    notice.set_timeout(TIMEOUT)

    notice.show()

    return



def cmdLine(argv):

    title = 'NEW MESSAGE'

    message = '{0} New Messages'.format(argv[0])

    sendmessage(title,message)



if __name__ == '__main__':

    if (int(sys.argv[1]) > 0):  

        cmdLine(sys.argv[1])

then I saved it in my /home/user_name/bin/ as "mailnotify"

Then in that field in the preferences of the Fire Tray plugin I typed the full path to the script, in my case, /home/jesse/bin/mailnotify.

Works like a charm now. I wanted to just change a parameter in a config file but oh well.

Hope this helps some one else out.

(The timeout parameter doesn't seem to do much, so if anyone could correct me that would be great)