They will unstablize but not much...you shouldn't be opening it the inc for that long. You can speed up the process by using warm water to start in the incubator...right now you are trying to warm the boxes to 87 (or whatever temp)...the closer the water is to this temp the less condensation you will have. Also make sure the fan isn't blowing on the boxes causing the side to cool down. Also, side condensation isn't an issue only the stuff on the lid (that could drip) needs to be worried about.

Hope this helps.