My Les Paul has the same problem (if you can call it a problem). The G and B strings are usually out of tune when I pick up the guitar. The cure? Get the guitar warmed up by playing it for a few minutes (mine can take about 20 minutes to stabalize). Make sure you do a lot of bends too, to make sure you stretch the strings.

Also, keeping it in the case will reduce the effects of temperature variations.

Every guitar has a quirk or personality as I call it, you just learn to live with it and find work arounds

Itchin' to play,

Izzy