converted comment to answer
I can't reproduce your problem - however the following may help:
Running applications through the Startup Applications GUI can sometimes be problematic - the GUI interface is being loaded at the same time as the applications specified in the Startup Applications.
Occasionally you can get unfortunate interactions such as your Thunderbird observation.
In my-case, I have pidgin or empathy started through the GUI but these applications did not display correctly.
The workaround I used was to introduce a short delay to allow the Unity/Gnome-Shell interface to be brought-up fully before pidgin or empathy was started.
Can I suggest you try something similar for Thunderbird - for the Startup-Applications command line entry
thunderbird change this to:
bash -c 'sleep 15 && thunderbird'
The command delays the startup of thunderbird by 15 seconds - if it works for you experiment with reducing the
sleep 15 value to give you the optimum shortest delay for starting Thunderbird.