Why the scripts (JS) are not generated by the master page?

If the scripts are not working or they are not generated, the reason is that your code is not valid.  You are probably using the following notation:

<script src="~/CMSScripts/Custom/MyScript.js"></script>

But the correct and valid notation is:

<script type="text/javascript" src="~/CMSScripts/Custom/MyScript.js"></script>

For more details, take a look at W3C tag script or Mozilla Developer, Kentico is using the XHTML by default.
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Martin Danko

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