Some modules will not send out emails if it tries to compile an email list and an email exists but is badly formed. These can be difficult to track down, especially if the email field is being pulled from Active Directory.
The easiest way to track down which emails are the culprits is to use the Email Users tool.
OPTIONAL: To prevent users from receiving a flood of email, you can change the SMTP server before doing this. It will prevent any emails from being sent from the portal. You can change it back immediately afterward.
To access the Email Users tool, go to the Portal Headquarters (default start page), expand the My Organization double down arrow, and click Email Portal Users. If you are not using the Headquarters as your start page, you can get there by going to http://portalname/Modules/Standard/SendEmail.aspx
Once there, add everyone to the list on the right by clicking Add All >> and give the email a subject and body. Then click Send to send.
You'll receive a list of users the email was sent to successfully and a list of users it was not, which will look like this:
, System - no email address provided in user profile
Email, Wrong - does not have a syntactically valid email address
Testuser, testuser - no email address provided in user profile
Users with no email show the first and last message. Users with email that doesn't fit the syntax of an email address will give the middle message. These are the users that are causing the emails not to be sent. Fix these emails up in these user's profiles or in Active Directory, and emails will start to be sent again.