There is a little recognized phenomenon called atmospheric vapor pressure, or barometirc pressure, that effects all bators.
The incubator as we employ it, is essentially a box open to the atmosphere through the vents, which we heat and attempt to condition to our needs.
But we do nothing to seal the box from changes in vapor pressure. Thus any passing storm front or atmospheric change in barometric pressure affects the ability of the air in the chamber itself to hold moisture vapor (relative humidity). This also affects, the temperature to a lesser extent, as the two are inter-related.
As long as you use the simple incubator as we know it, you will be faced with this problem. I would make two suggestions that may help:
1. Monitor both room humidity and barometric pressure, in addition to the humidity in the chamber. This way you will begin to see a correlation between the two and have advance warning of changes that will ulitmately be seen in the chamber.
2. Learn about the "Dry Incubation" method and understand how it's main points apply to your situation.
I hope this is of some use.