I had the following in a header:

===
struct _GuestfsVersion {
  gint64 major;
  gint64 minor;
  gint64 release;
  gchar *extra;
};
typedef struct _GuestfsVersion GuestfsVersion;

GType guestfs_version_get_type(void);
===

which generated the following in the .gir:

===
    <glib:boxed glib:name="Version"
                c:symbol-prefix="version"
                glib:type-name="GuestfsVersion"
                glib:get-type="guestfs_version_get_type">
    </glib:boxed>
    <record name="_Version" c:type="_GuestfsVersion">
      <field name="major" writable="1">
        <type name="gint64" c:type="gint64"/>
      </field>
      <field name="minor" writable="1">
        <type name="gint64" c:type="gint64"/>
      </field>
      <field name="release" writable="1">
        <type name="gint64" c:type="gint64"/>
      </field>
      <field name="extra" writable="1">
        <type name="utf8" c:type="gchar*"/>
      </field>
    </record>
===

This does not allow introspected access to the fields of Version.

I altered the header by moving the typedef before the struct declaration:

===
typedef struct _GuestfsVersion GuestfsVersion;
struct _GuestfsVersion {
  gint64 major;
  gint64 minor;
  gint64 release;
  gchar *extra;
};

GType guestfs_version_get_type(void);
===

This results in the following, correct output in the .gir:

===
    <record name="Version"
            c:type="GuestfsVersion"
            glib:type-name="GuestfsVersion"
            glib:get-type="guestfs_version_get_type"
            c:symbol-prefix="version">
      <field name="major" writable="1">
        <type name="gint64" c:type="gint64"/>
      </field>
      <field name="minor" writable="1">
        <type name="gint64" c:type="gint64"/>
      </field>
      <field name="release" writable="1">
        <type name="gint64" c:type="gint64"/>
      </field>
      <field name="extra" writable="1">
        <type name="utf8" c:type="gchar*"/>
      </field>
    </record>
===

The above C is semantically equivalent, and the g-ir-scanner behaviour should be identical in both cases.