I realize this has been almost 10 years, but
do you happen to have the code that you implemented
that showed this problem?

To test and verify this isn't an issue anymore, I ran demo.py and
modified the tracker to use:

<tr tal:condition="context/is_edit_ok">
 <th i18n:translate="">Change Note</th>
 <td colspan=3>
  <textarea tal:content="request/form/msg-1/value | default"
            name="msg-1@content" wrap="hard" rows="5" cols="80"></textarea>
    <input type="hidden" name="@link@messages" value="msg-1">
    <input type="hidden" name="msg-1@author" value="admin">
    <input type="hidden" name="msg-1@date" value=".">
 </td>
</tr>

<tr tal:condition="context/is_edit_ok">
 <th i18n:translate="">Change Note 2</th>
 <td colspan=3>
  <textarea tal:content="request/form/msg-2/value | default"
            name="msg-2@content" wrap="hard" rows="5" cols="80"></textarea>
  <input type="hidden" name="@link@messages" value="msg-2">
  <input type="hidden" name="msg-2@author" value="admin">
  <input type="hidden" name="msg-2@date" value=".">
 </td>
</tr>

to basically duplicate the @note field (replace the exiting Change Note
named @note with the above). This should create two messages if you put
content in both text boxes.

When I do this, I see both messages created and linked to the
messages multilink for the issue.

So I am marking this works for me in absence of any other info
that I can use to reproduce your issue.