I'm not sure if blizzard saves scaling settings in its auto save files.
I know it stores the position and sizing although not always the position and size you were planning on rofl. The blizzard cvars and saved variables are loaded with VARIABLES_LOADED or rather that event is triggered once they have finished their stuff rofl.
You could use that to see if frame:GetScale() returns what you initially used frame:SetScale() with. That would the first step to see if it ignores the scaling you did or if it deals with it but does something different rofl.
As to using your own SavedVariables. wowwiki is a good resource for that. This page may help you figure that stuff out if it works out that you need to use it :
http://www.wowwiki.com/Saving_variab..._game_sessions
Also, on a side note, from what I found out while playing with the watch frame positioning and sizing etc there is a file called layout-local.txt in your characters wtf folder that seems to be where they store the individual layout of some but not all frames.
Ah, here it is. The frame layouts stored there seem to be done if you use the function
http://www.wowwiki.com/API_Frame_SetUserPlaced and there are a few key conditions that you might want to see if that could be why it doesn't work for you.
However, like I said, I doubt that it stores the scaling. Here is an example of one of the frames for one of my characters:
Frame: MinimapCluster
FrameLevel: 6
Anchor: BOTTOM
X: -6
Y: 30
W: 192
H: 192
A quick search for scale and a scan for anything that could mean scale found nothing in the file.
So worst case scenario you will need to store and restore the scaling.