I had the same symptoms, though a different set-up. (See at the bottom.) This appears to be fixed now. The key was to disable Unity's application switcher and re-enable compiz's static switcher.
Warning - you can mess up your desktop doing this. Don't try it when there is a possibility you will accidentally click on the wrong thing (due to using a laptop track-pad or (like me) having toddlers who may randomly mash your keys before you can stop them). Don't try it if you are not capable of fixing a locked-up machine if things go wrong. Caveat Emptor. See: What are some of the issues with ccsm and why should I not use it?
Here are the steps I took:
sudo apt-get install compizconfig-settings-manager
Disable the keyboard shortcuts for Unity's switcher by unchecking the following check-boxes in CompizConfig Settings Manager ▸ Desktop ▸ Ubuntu Unity Plugin ▸ Switcher:
- Key to start the switcher ▸ Enabled
- Key to start the switcher in reverse ▸ Enabled
- Key to start the switcher for all Viewports ▸ Enabled
- Key to start the switcher in reverse for all Viewports ▸ Enabled
Enable the Static Application Switcher by checking CompizConfig Settings Manager ▸ Window Management ▸ Static Application Switcher ▸ Enable Static Application Switcher
- There shouldn't be conflicts if I remembered all the ones had to resolve. However, if there are key-conflicts, remove the one for the unity plug-in.
- There was quite a delay (30 seconds-1 minute) during which my machine was unresponsive while the static switcher enabled. Don't click on anything during this time, the clicks will be cached and played back.
My answer is indebted to the accepted answer to: How do I revert Alt-tab behavior to switch between windows on the current workspace?
The difference in my setup was that I installed Eclipse Indigo /Java EE manually (with my own .desktop file) and did not install Py/Dev, but I was having the same problems - no carets on the Unity launcher, and Eclipse did not appear in Alt-tab - the only way to switch to it was Super-W.