Referring to the data you provided (taken emergency birth control pill, previous irregular periods due to sex hormonal problems and treated with medications), your girlfriend might expect that the pill she took after the intercourse would affect her regular medications. Both the emergency birth control pill and the medications that are used to treat the irregular periods are highly likely to contain hormones (no generic name or brand provided).
This might mix the hormonal presence in the blood, which levels try to be maintained, with the regular hormonal medications. The menstrual period might become more irregular due to this. However, the condition might be treated with other hormones that would be given in appropriate dosage and regimen in order to try to make the menstrual periods regular.
Your girlfriend might want to wait and see if her menstrual periods get worse or do not become more regular with the usual medications. If this happens, she might want to visit her gynecologist to determine the most adequate hormonal treatment.