The default location for storage of AutoText is the Normal template.
I would suggest that when you start Word using the icon, it is not using the template with your AutoText.

Here is how to find which normal.dotm template is being used:
Where is the Normal Template / How to Find the Normal Template
(Use the vba method.)

When you open Word using the Icon, you should be able to use the Organizer to copy AutoText from an old normal.dot(m) file or other template.