When TC'ing a COT, a warning message is produced saying this COT overlaps with another.
Go to the patients transactions (£ button) and check the date of the last FP17.
If the dates of the new COT and the last do not overlap, then TC through and ignore the message. You will be paid as you should.
Also check in the Chart History that there is not already a Course of Treatment that has been created on the same day with the same treatment.
If the courses do indeed overlap, contact the board as you may not be paid for both courses.