If completed courses are not going to the transcript as expected, please check the following things:
1) is there a mark in the official mark column? (and it is generally the right mark?)
2) is the 'done' box checked?
3) does the class's end date fall within the dates you're choosing?
#2 and #3 are straightforward to figure out, but #1 can be tricky. Please check the following things:
a) achievement parameters, make sure a mark 'can go' into the highlighted areas here (this is an Ontario specific example, but the disabled pieces need to be changed to the appropriate letter grade group:
Once that is fixed and synchronized out to the school(s), you may have to run a recalculate to get the mark to populate into the official mark column.
b) achievement parameters #2, even if everything looks OK, sometimes it works to 'refresh' the letter grade groups chosen there (set to something else, then back to the right one and save)