Formatting is controlled by Styles especially when a paragraph mark is included in the entry. The styles may be defined differently in different documents and templates. If the style is already in use (and perhaps directly formatted to look different from the style settings) its definition will overrule the definition originally used in the AutoText entry.
Automated Boilerplate Using Microsoft Word
For examples of styles altering appearance on inserted text, see the
tutorial on the IncludeText field. It behaves similarly to AutoText. Especially look at the part on Styles.
For more about Styles, see
Understanding Styles in Microsoft Word