- It is expected that the function appears empty in the screenshot since i removed all Js code and Direct Methods removed to make things simpler. Same thing happens if there is any code between the tags).
Ah, okay. Thank you for clarifying.

Please try the following. There is Ext.Net\Core\InitScriptFilter.cs file. Please set a breakpoint on the line #77 inside the Transform method.
protected virtual string Transform()
{
    return ExtNetTransformer.Transform(HttpContext.Current.Response.ContentEncoding.GetString(this.htmlList.ToArray())); // here
}
Please post the result of
HttpContext.Current.Response.ContentEncoding.GetString(this.htmlList.ToArray())
and
ExtNetTransformer.Transform(HttpContext.Current.Response.ContentEncoding.GetString(this.htmlList.ToArray()));
for the problematic page.

For example, I tried with this simple page.

Example
<%@ Page Language="C#" %>

<!DOCTYPE html>
<html>
<head runat="server">
    <title>Ext.NET v3 Example</title>
</head>
<body>
    <form runat="server">
        <ext:ResourceManager runat="server" />
    </form>
</body>
</html>


Before transformation
(additional manual formatting was applied to improve readability)
<!DOCTYPE html>
<html>
<head>
    <title>Ext.NET v3 Example</title>
</head>
<body>
    <form method="post" action="Work3.aspx" id="ctl01">
        <div class="aspNetHidden">
            <input type="hidden" name="__EVENTTARGET" id="__EVENTTARGET" value="" />
            <input type="hidden" name="__EVENTARGUMENT" id="__EVENTARGUMENT" value="" />
            <input type="hidden" name="__VIEWSTATE" id="__VIEWSTATE" value="/wEPDwUKMTc1OTU1NjkzNmQYAQUeX19Db250cm9sc1JlcXVpcmVQb3N0QmFja0tleV9fFgEFBWN0bDAzdX2wS05fQK2ohA5LlrJnJ+rasJgnLacyAAhcw2QXcJA=" />
        </div>

        <script type="text/javascript">
            //<![CDATA[
            var theForm = document.forms['ctl01'];
            if (!theForm) {
                theForm = document.ctl01;
            }
            function __doPostBack(eventTarget, eventArgument) {
                if (!theForm.onsubmit || (theForm.onsubmit() != false)) {
                    theForm.__EVENTTARGET.value = eventTarget;
                    theForm.__EVENTARGUMENT.value = eventArgument;
                    theForm.submit();
                }
            }
            //]]>
        </script>

        <div class="aspNetHidden">
            <input type="hidden" name="__VIEWSTATEGENERATOR" id="__VIEWSTATEGENERATOR" value="3FB72D2A" />
        </div>

        <#:item selector="headstart" index="20">
            <script type="text/javascript" src="/extjs/ext-all-debug-js/ext.axd?v=29937"></script>
            <script type="text/javascript" src="/extjs/packages/ext_theme_gray/build/ext-theme-gray-debug-js/ext.axd?v=29937"></script>
            <script type="text/javascript" src="/extnet/extnet-all-debug-js/ext.axd?v=29937"></script>
        </#:item>

        <#:item selector="headend">
            <script type="text/javascript">
                //<![CDATA[
                Ext.net.ResourceMgr.init({id:"ctl03",aspForm:"ctl01",theme:"gray",locale:"en-US"});
                Ext.onReady(function(){
                    <#:anchor id="ExtNetOnReadyBegin" />
                        <#:anchor id="init_script" />
                    <#:anchor id="ExtNetOnReadyEnd" />
                });
                //]]>
            </script>
        </#:item>
        
        <#:item selector="headstart" index="10">
            <link type="text/css" rel="stylesheet" href="/extjs/packages/ext_theme_gray/build/resources/ext-theme-gray-all-embedded-css/ext.axd?v=29937" id="ext-theme" />
            <link type="text/css" rel="stylesheet" href="/extnet/resources/css/extnet-all-debug-embedded-css/ext.axd?v=29937" id="extnet-styles" />
        </#:item>
        
        <ext.net.initscript.warning>
            <script type="text/javascript">Ext.onReady(function(){Ext.Msg.show({title:'Warning',msg:'The <code>web.config</code> file for this project is missing the required DirectRequestModule.<br /><br /><div style="margin-left:48px;"><b>Example</b><br /><br /><code>&lt;system.web><br />&nbsp;&nbsp;&lt;httpModules><br />&nbsp;&nbsp;&nbsp;&nbsp;&lt;add name="DirectRequestModule" type="Ext.Net.DirectRequestModule, Ext.Net" /><br />&nbsp;&nbsp;&lt;/httpModules><br />&lt;/system.web></code><br /><br />More information available at "<a href="http://examples.ext.net/?/Getting_Started/Introduction/Overview/">Getting Started</a>".</div><br />',buttons: Ext.Msg.OK,icon: Ext.MessageBox.WARNING});});</script>
        </ext.net.initscript.warning>
        
        <#:item selector="warning" />
        
        <#:item selector="viewstate" />
        
        <#:inputs ref="init_script" index="-100" />
        
        <#:item selector="postback" />
        
        <#:item selector="removeblocks" />
        
        <#:item selector="removeLeadingEmptyLines" />
        
        <#:item selector="removeLeadingEmptyLinesAfterForm" />
    </form>
</body>
</html>


After transformation
(additional manual formatting was applied to improve readability)
<!DOCTYPE html>
<html>
<head>
    <link type="text/css" rel="stylesheet" href="/extjs/packages/ext_theme_gray/build/resources/ext-theme-gray-all-embedded-css/ext.axd?v=29937" id="ext-theme" />
    <link type="text/css" rel="stylesheet" href="/extnet/resources/css/extnet-all-debug-embedded-css/ext.axd?v=29937" id="extnet-styles" />
    <script type="text/javascript" src="/extjs/ext-all-debug-js/ext.axd?v=29937"></script>
    <script type="text/javascript" src="/extjs/packages/ext_theme_gray/build/ext-theme-gray-debug-js/ext.axd?v=29937"></script>
    <script type="text/javascript" src="/extnet/extnet-all-debug-js/ext.axd?v=29937"></script>

    <title>Ext.NET v3 Example</title>

    <script type="text/javascript">
        //<![CDATA[
        Ext.net.ResourceMgr.init({ id: "ctl03", aspForm: "ctl01", theme: "gray", locale: "en-US" });
        Ext.onReady(function () { });
        //]]>
    </script>
</head>
<body>
    <form method="post" action="Work3.aspx" id="ctl01">
        <div class="aspNetHidden">
        </div>

        <div class="aspNetHidden">
            <input type="hidden" name="__VIEWSTATEGENERATOR" id="__VIEWSTATEGENERATOR" value="3FB72D2A" />
        </div>
    </form>
</body>
</html>