I ran in to this issue yesterday, and thanks to Luis Benitez and David Hay for steering me in the right direction.

This problem on occurs in multi-node deployments of IBM Connections, and fortunately there is a fix out there for both 3.0 and 3.0.1.

“Problem Users are receiving multiple copies of email digests sent from scheduled daily/weekly task ‘EmailDigestDelivery’.

Problem description The problem occurs on a multi-node deployment. The bug is in the load balancing (same scheduled delivery tasks is running in parallel on the different nodes) of scheduled tasks logic. Apply this iFix to address the load balancing problem in ‘News’ application. “

APAR L060006: RECEIVE DUPLICATE COPIES OF EMAIL DIGESTS

Direct Link to the fix

The first Lotus Connections 3.0 fixes are available on Fix Central, the first one L057305 “INSTALL: Resolve forum migration issue when using dbWizards GUI mode.” is important (see below for instructions) you should address before running your Database Wizards.  The second ne L057308 “INSTALL: Change server names post install for Lotus Connections 3.0.” is optional (see below for details) but is only needed if you want to change your server names after installation.

There are links for more information on each fix with instructions

L057305

“Install Instructions:
Before you executing db wizards, only need to unzip LO57305.zip and replace the Wizards.jar file with the new file in Wizards/lib directory, i.e E:\LC3.0\Wizards\lib”

L057308 – This one is optional, you only need it if you want to rename your WAS Server names after installing Lotus Connections 3.0 – good to know it’s there should you need it, better plan ahead and get your names right before installing.