There is a Known Issue with Alert Manager 2010 in some environments where users are unable to use custom templates when creating alerts. Instead, the template reverts to the default template for the type the alert is being created for (document libarary, calendar, etc.).
There is no known resolution date and no workaround for the issue at this time.
** PLEASE NOTE - Our Known Issues are numbered by the support ticket that led to the creation of the forum post and are not cumulative in regards to total issues for a specific product **