Comment 12 for bug 1181666

I'm having the same problem after upgrading from 13.04 with Gnome-Shell 3.8 to 13.10 with Gnome-Shell 3.10. I do not use Pidgin.

In my experience, the problem is consistently reproducible when the Overview is exited by clicking on an application. When I select any running application on any Workspace, all applications fail to respond to any mouse input. If I, from the Overview, click to show the Desktop (thanks to the Show Desktop From Overview extension), then Alt-Tab to a running application on that Workspace, I don't encounter the issue.

However, I have found one way to quickly recover which is to activate the Google Chrome browser (which I always have running) and switch tabs via the Ctrl+Pg[Up|Down] keyboard shortcut. I find that it usually takes a couple switches Up and Down, irrespective of which direction I go (i.e. I almost always must go both directions). I happen to have had these keyboard shortcuts bound to the left & right tilt of my Logitech MX Revolution mouse wheel for quite a long time, even before the upgrade, using xbindkeys.

I've performed some extensive testing and my conclusion is that the issue is somehow caused by Chrome, or perhaps the fact that Chrome is resident in memory, consuming 2.7 GB of RAM currently according to Chrome's own internal reporting. I've tried disabling all Gnome-Shell extensions which had no effect. I next tried disabling all Chrome extensions which had a small, but noticeable, effect. The only thing that seems to have dramatically abated the issue is not having Chrome loaded at all.

Here are my system specs, in case it's relevant:
Power:
  RAIDMAX HYBRID 2 RX-730SS 730W ATX12V V2.2/ EPS12V SLI Ready CrossFire Ready Modular Power Supply
Motherboard:
  ASUS M5A97 AM3+ AMD 970 SATA 6Gb/s USB 3.0 ATX AMD Motherboard with UEFI BIOS
CPU:
  AMD FX-8120 8-core 3.1 GHz CPU
RAM:
  Mushkin Enhanced Essentials 16GB (2 x 8GB) 240-Pin DDR3 SDRAM DDR3 1333 (PC3 10600) Desktop Memory
Display:
 Video:
  MSI R6570-MD2GD3/LP Radeon HD 6570 2GB 128-bit DDR3 PCI Express 2.1 x16
 Output:
  Insignia 42" LCD HDTV connected via VGA, running at 1920x1080 resolution (1080p)
Storage:
1 x WDC WD10EZEX-00RKKA0 1.0 TB SATA HD used as OS / Home
4.5 TB BTRFS storage array comprised of:
2 x ST31500341AS 1.5 TB SATA HD
1 x ST31500541AS 1.5 TB SATA HD

I think my video card is the weak point and that it needs to be upgraded. After upgrading to 13.10 I did install the latest ATI proprietary video driver direct from their website. Prior to upgrading I had been using the latest Ubuntu-provided binary driver. That may also be a factor, but I haven't tested it.