Sounds like a classic case of the intonation drifting off, due to the neck being effected by the weather change. Or, it's been too long since the guitar's had a pro setup, or you've messed with some aspect of the setup that negatively effected the intonation.
Refer to the intonation thread in the Vault. Anytime you have tuning issues, the first place to go is a thorough re-intonation. That means making sure that all the notes on the fretboard read as close to dead center on a tuner as possible.....not just the open and 12th fretted notes.