I'm running Ubuntu 13.10 in VirtualBox. The host machine is running Windows 7 with an ATI Radeon HD 5570 video card, 12 GB of memory, 2 quad core i7 CPUs. I've given the virtual machine 4GB of memory, 128 MB of video memory, 1 CPU, and checked the 3d acceleration box in VirtualBox (without 3d checked everything runs like molasses in the winter time).
Every 5 or 10 minutes some of my windows start flipping between a chrome state (the title bar is visible) to a no chrome state (the title bar disappears) which makes the windows jump up and down. This happens with Chrome, Firefox, and Sublime which are pretty much the only apps I use on this box. For Chrome and Firefox, if I delete the user preferences folder then it temporarily seems to fix things. But now it started with Sublime and I haven't found a good fix yet which means I can't currently do any work.
Here is a .gif of the problem:
Why is this happening and what do I need to do to permanently fix it?