From my understanding, for ITA points, it does not matter whether you are in FSW or CEC. Canadian work experience and foreign work experience both give you points in different categories. If the officer decides that your Canadian or foreign work experience does not fulfill the requirement, they will re-calculate your points, independent of what their computer system tells you. In fact, they calculate points based on what the law says, not what their computer system says. Therefore, the problem that you faces is probably that after their re-calculation, your point is not at or above the invitation points. Therefore, no matter whether you are in FSW or CEC, your application will not be processed if your point is below the invitation points.
I have been rejected in the past. As long as you have valid authorization (work permit or study permit), they will still admit you into Canada.
