Alert Manager will not send daily or summary alerts when using a custom alert handler. The latest version should prevent the creation of custom alerts with the summary (daily, weekly) frequency.
Regarding alerts to SharePoint Groups, there are a couple of items you should check..
1. Does you alert have an owner or is it unassigned? The new version assigns SharePoint Group alerts to the user creating the alert. If the alert is not assigned it will not be sent out. Please delete the existing alert and recreate it.
2. Does the owner of the alert have permission to the list or list item?
3. Do the members of the SharePoint Group have e-mail addresses defined in SharePoint?
4. Did you restart the Windows SharePoint Server Timer service when you performed the upgrade?
Jeremy Luerkens
Manager, Software Production
SharePoint Solutions