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

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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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