I use above (nearly) every page a script (see url). The <script></script> tag has a src= attribute but no content. The script is enclosed in a <span></span> tag to control the presentation. The hierarchical tree is thus <span><script></script></span>.
Amaya pretends to put the <span></span> as content of the script: <script><span></span></script>. As a result, the presentation is lost and the script also, <span></span> being no legitimate JavaScript code!

Code is as follows :
<p>
  <span class="floatleft smaller">
    <script type="text/javascript" language="JavaScript" src="../monAdresse.js">
    </script>
  </span>
</p>

1. Amaya is unable to display the page correctly (compare with Firefox).
2. Upon editing anything in the page Amaya transforms the code in the nonsensical

<p><script type="text/javascript" language="JavaScript" src="../monAdresse.js">
<span class="floatleft smaller"> </span></script></p>

This makes Amaya practically unusable with scripts.

In my distibution (Ubuntu 8.04), the version provided is Amaya 9.55 Feb 13 2008.
I tried different versions (10.0, 10.1.pre3, 10.1.pre4) and found the same destructive behaviour.
(First filed on Sun, 13 Jul 2008 19:12:45 +0200 as "Amaya messing up a script and a span" in the www-amaya@w3.org list.)