Upon waking up, sometimes the Mac jams all of my icons into one corner, and throws some windows almost completely off the screen or makes them really small. This happens frequently often on 2 systems, yet I haven't found many people asking about it online.
Sometimes I haven't even unplugged the machine, it's just it sat for a few hours and decided to goto sleep.
As an example, when I move the mouse in the morning, many of the Safari windows are now only a couple hundred pixels high and I have to drag the bottoms to resize. And if I don't do that to all of the and open another window, it too is very short.
I have a Retina Macbook and a MacBook Air. Both machines are almost always closed and feeding external monitors (either Thunderbolt display or HDMI monitor)
The macs are up to date.
I did see posts about .DS_store but I don't think they don't seem to match the symptoms I'm seeing.
I think OS X has some fancy way of moving Windows and Desktop icons around relatively when the screen resolution changes, which is nice most of the time.
HOWEVER, I think gets confused about how big the screen is when undocking or sleeping, so it thinks it has a tiny screen, which it can properly place icons on but records those new bogus positions, and then when it's back on a big screen, scales back up those mistakes.
It seems silly that this event gets it so confused about its screen size (if that's the issue) Perhaps when it's going to sleep, it briefly thinks it's going from 1 monitor to 0 monitors, and that the resolution is now 0x0 ? Or maybe this happens in a split second when it's waking up.
I think the real fix is for OS X to not pay attention to screen resolutions that are obviously nonsense, or to not attempt to resize when there are "no" monitors.
So maybe there's some setting to tell OS X to ignore screen sizes that are below some tiny threshold?
Another idea would be for a utility that we record relative positions and let me reset the desktop icons to some previously sane state.
Still happens with open windows on Mavericks. For example, last night my machine was left plugged in, so just had to wake it up this morning.
But the VirtualBox window was shoved to the far lower right corner, barely visible at the very far edge of the Dock. Almost the only parts visible were the red, yellow and green dots of the window frame. With very careful aim and several attempts, I was able to click on some of the gray pixels of the window border and drag it back up. And now the window was size of 2 postage stamps side by side.
Obviously there's a workaround to carefully drag the window back up and resize it back to normal. But I didn't even undock the machine! I double checked my power settings just now, when plugged in it's set to Never sleep, and it was just the Display that's set to sleep after 3 hours. So it's JUST the screen switching off that does this - it's crazy, and I'm really surprised more people aren't seeing this.