Hi Tom,
First off I take it you have created a learning plan and its set as the default template.
Then you create your postional and/or organisational hierarchies.
Then you associate competencies with the relevant hiearchies, and courses with the competencies.
Learners should be assigned position and/or organisation & manager under Positions>Primary position.
The courses should then automatically appear in the learner's learning plan.
I think first off Id check all the start date/finish dates are correct in the courses, learning plan and for the learners.
Please get back to me and let me know how you get on.
regards,
George.