On Moodle 2.6, when I used 1 file that referenced more than 1 template course, it did not work as expected for any course that referenced the second template course.
Ex: if I had 5 lines in the excel file that were to use template course A, and 3 more lines that were to use template course B, only the first 5 lines would end up looking as expected. The additional lines created courses that did not look correct (i.e. Wrong blocks and wrong number of parts). I have not tried one big file ever since (if I was using different template courses), so not sure about this behavior on 3.0
Did the first course look correct, or both courses? Can you try 2 separate files? One for the 1st template course and one for the 2nd template course and see how that looks?