Always an inconsistent logic with DisableAutoFormatting:

 

With:

<Script language="javascript">
   var Ni = 2;
   for(i=0;i<Ni;i++){Ni=Ni;}
</Script>
<Div ID="Test"></Div>

--------------------------------------------------------------

DisableAutoFormatting=false : ConvertHTMLTagstoLowercase=false

<Script language="javascript">
   var Ni = 2;
   for(i=0;i<Ni;i++){Ni=Ni;}
</Script>
<div id="Test"></div>

--------------------------------------------------------------

DisableAutoFormatting=false : ConvertHTMLTagstoLowercase=true

<Script language="javascript">
   var Ni = 2;
   for(i=0;i<Ni;i++){Ni=Ni;}
</Script>
<div id="Test"></div>

--------------------------------------------------------------

DisableAutoFormatting=true : ConvertHTMLTagstoLowercase=false

<Script language="javascript">
   var Ni = 2;
   for(i=0;i<Ni;i++){Ni=Ni;}
</Script>
<DIV id=Test></DIV>

--------------------------------------------------------------

DisableAutoFormatting=true : ConvertHTMLTagstoLowercase=true

<!--{cps..0}-->
<div id=Test></div>