In v2.8 custom fields were only for tasks.
In v3.0 custom fields can be created both for tasks and task groups.
You say "We have several folders (groups) that have a custom field that has data entered." Please explain what you mean.
1. You updated to v3.0 and created custom fields for Task Groups, but when you open Edit Task Group window there are no custom fields?
2. You didn't create any custom fields for Task Groups but on the Task Tree view you see that Task Groups have custom fields and values entered?
In v3.0 custom fields for Task groups should be set by the way described here:
http://www.taskmanagementsoft.com/products/taskmanagerpro/help/how-connect-custom-fields-with-task-group.php
Please take a look at this page and see if it can help.