Ive had similar problems with all of my thinner necks, allthough maple seems to be quite resistant to temerature changes. As such it seems to me that dampnes + temp changes are what the problem is. A well oiled fretboard does more or less eliminate the damp factor IMO.
Things that i do to eliminate this is keeping the fretboard oiled with the dunlop citrus oil, which is very nice IMO, use form cases with plenty neck support all over and store with the neck in upright position. It seems that string tension plays a part in this (metal responds more to temp changes than wood) so maybe backing off the tension
a bit prior to storing might do it. Also did you put the guitar against the outside wall or the inside wall? Usually there is more temp changing when put against an inside wall, or well kind off depends on how you heat your house probably.
I once tried storing a guitar with the thrussrod loosened and without strings, not a very bright idea..... It might make a bit of difference to tighten the thrussrod a bit more, the guitars i have that are set up the tightest also repond least to temp changes.
Also, Elixer strings have less string tension, a .10 compares to a .09 set so you can keep the feel of a .10 but play with lesser tension which can be nice on a petite eggle.
Anyway, my 2 cents on the subject, if i buy a guitar which i know has been hanging in the shop long i would always soak the fretboard thoroughly with oil. Mostly they are very dry from the shops heating. Probably you know all this stuff, but like i said, just saying how i do it since i live in an even older house....
With a bit of care it should be perfect resting in its case, oh yes, if you dont have a form case and had the guitar laying down on its back its probably just that.
The longer i play the more i like
FAT necks :lol: 8)
EDIT: A full tremelo springload might add to the problem since the springs tighten when it gets colder.