Many hormone-containing birth control pills might cause changes in the menstrual period as side effects. The changes might include variations in length of menstrual cycle, length of menstrual period or changes in the blood loss (light or heavy periods).
Changing how you take birth control pills increases the chances of these side effects happening. That is why the pills have to be taken in the exact regimen recommended by a gynecologist or found on the leaflet in the package.
Given the data you provided (period only 3 days in September about month after stop taking pills in mid August, no period at all in October), you might be experiencing side-effects. Your body might need additional time to restore the regular hormonal production which is not supported by the pills now.
However, you might want to visit a gynecologist for a physical examination, hormonal laboratory tests and ultrasound scan of the ovaries just to make sure.