Hi,
Ive come across what I believe could be a bug, however I could be mistaken. I will do my best to describe what I have found.
I had my game settings to a resolution of 1024 x 768. I wanted to change it to 640 x 480 temporarily, to test something out. When I finished, I reverted it back to 1024 x 768.
I noticed then that all my GUI's buttons have been moved, and resized, etc...
So I decided to quit AGS without saving so I could get back my previous version.
When I re-opened AGS, and my game...I found that is saved AFTER everything got resized, etc...as if the "dont save" function didnt work.
I tried reproducing this bug and I successfully reproduced it each time (3 times).
If this is indeed a bug, I would say its a MAJOR one because I had to basically reset all the button's positions and the GUI sizes, which is a real bi*atch!! :P
When you change the resolution, AGS gives you the option to automatically resize your GUIs (scale them up or down) for the new resolution. Is it possible you accidentally clicked through the confirmation popup without noticing? I think it saves when you change res, and of course if you tested the game (via F5) - so not saving when you exit wouldn't have any effect (the 'damage' was already done). I don't think resizing the GUIs when you tell it to counts as a bug, as much it CAN be a bi*tch if you didn't mean to :), but of course if you clicked 'No' to resizing, then it is indeed a bug.
EDIT:
Actually, I just realised - it should've upscaled the GUIs when you changed back, unless you told it NOT to then. Which might make it less likely that you just made the same mistake I did ::), and more likely you encountered a legitimate bug...
If you change the res back to 640x480 without scaling the GUIs, then back up to 1024x768 with scaling, do they get fixed?
Are you sure you didn't test the game (using F5) which as GuyAwesome says would have saved it?