I have been having an issue when Nexus is running alt-tab does not cycle through all running apps. After a reboot everything works but after a while it will only cycle through a short list of running apps or not cycle at all.

I used the Nexus option to reset my settings (but keeping my docks) and the problem has gone away.

I have no idea what setting caused the issue but even after changing some of the defaults to my liking it continues to work.

Now, if only the main launch dock was more responsive, everything would be great! The running and system tray docks appear immediately but the launch dock can take several seconds.

Interesting. It also fixed the other issue I've had with the blank icon in my running apps dock.

Hmmm... it would be useful if the setting or function causing the problem (assuming there is indeed something) could be identified.