My 13 month old has suddenly started having sinus problems, what is causing this?

Keep in mind, 13 month olds have not developed sinuses yet (except for very, very tiny ethmoid sinuses by their eyes). So this is likely not a "sinus" issue. However, because of lack of sinuses, there is little area for mucous to go, so it congests the nose, the ears (causing ear infections) and down the throat, causing a cough. I think it sounds like allergies or irritants are really reaking havoc with your baby's nose. A 3 day reprieve from this is not long enough to help cure the symptoms at this point. You either have to permanently leave, or consider other medications. You're doing everything right. However, you may have to add prescription antihistamines or nasal steroid sprays, both of which are indicated down to 6 months of age, by seeing your pediatrician.