Sounds to me that it's an humidity issue since the humidity is lower in winter, humidity issue is an allergic reaction to mold and spores in a sense that it lays unrest on the body and the metabolic rate is affected and exhausted, nutritional imbalances follows and you start to think it's the food that ails.
I have read several similar stories where people have moved into new houses and apartments just to get free of humidity and the mold it creates.
You could try to get someone check out the mold content of the air inside your apartment and if there is a find, it would be wise to take action (new carpets? dehumidifier?) or move to a new apartment.