"Sharepoint 2007 OTB "Alert Me" not working for some sites"

Hello All,
We are facing some problem with sharepoint OTB "Alert Me" functionality. When someone subscribes themselves to a list/library they recieve the first email telling them that you've been signed up for alerts. However, when any changes
are made to the list or library users are not receiving email alert about the update. This is not happeing on all sites. We are noticing this behaviour only on certain sites. Working and Non-working site collections are residing on the same web app.
We have checked below things from our side
1. SMTP and Timer service is running on 2 WFE servers
2. "Immediate Alerts" Timer Job is running as usual.
Please share your comments on the same.
Thanks in advance
Regards,
Bob

Check the date and time in the clock on your computer: (double) click the clock icon on the Windows Taskbar.
Check out why the site is untrusted and click "Technical Details to expand this section.<br>If the certificate is not trusted because no issuer chain was provided (sec_error_unknown_issuer) then see if you can install this intermediate certificate from another source.
You can retrieve the certificate and check details like who issued certificates and expiration dates of certificates.
*Click the link at the bottom of the error page: "I Understand the Risks"
Let Firefox retrieve the certificate: "Add Exception" -> "Get Certificate".
*Click the "View..." button and inspect the certificate and check who is the issuer of the certificate.
You can see more Details like intermediate certificates that are used in the Details pane.
If "I Understand the Risks" is missing then this page may be opened in an (i)frame and in that case try the right-click context menu and use "This Frame: Open Frame in New Tab".
*Note that some firewalls monitor (secure) connections and that programs like Sendori or FiddlerRoot can intercept connections and send their own certificate instead of the website's certificate.
*Note that it is not recommended to add a permanent exception in cases like this, so only use it to inspect the certificate.

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Try troubleshooting using the link
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Hi,
Whether all of the user can’t receive alert email in this site collection.
Check whether the "Immediate Alerts" time job is enabled for your web application.
Try to do restart SharePoint Timer services and IISReset.
Here are two articles about troubleshooting SharePoint alerts not working, you can use as a reference:
http://www.sharepointdiary.com/2012/02/sharepoint-alerts-not-working-troubleshooting-checklist.html#ixzz2aSvOz3hB
http://blogs.technet.com/b/steve_chen/archive/2009/11/20/alerts-in-sharepoint-troubleshooting-moss-wss.aspx
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"Sharepoint 2007 OTB "Alert Me" not working for some sites"

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