The provided information is not sufficient enough and we can not speculate on the reasons behind this behavior.
May I ask you to open a regular support ticket and provide a sample, runnable project that replicates the problem, so we can inspect it locally?
Currently, the only thing that I could suggest is that you debug your code and see if you are hitting the line where you call the Alert method. Additionally, you could elaborate on what exactly that Alert method does. If you have enabled AJAX for some controls, you could also try to temporarily disable it and see if the alert will be displayed.
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