Awesome! I am glad it worked. Of course, it begs the question, “why does the screen saver get uninstalled in some cases?”
An inventive hack, but … I wish Linux worked better sometimes and didn’t always need little hacks and tricks to get it to do what you want.

This is one of those annoying problems because “it works on my computer”.
This site, suggests the problem is that gnome-screensaver is not installed.
When I uninstalled gnome-screensaver I was able to reproduce your problem (although, there may be other reasons why locking the screen does not work).
To install gnome-screensaver either:
(1) enter it into the Ubuntu Software Center search field and select to install it or
(2) enter the command sudo apt-get install gnome-screensaver in a terminal.
I’ll be honest, I do not find it the least bit intuitive that a screensaver should be responsible for locking the desktop.
Please let me know if this fixes your problem (and thanks for the comment).

Interesting question, I have not experienced this problem – so it is hard for me to offer an answer if I can’t reproduce the problem.
I do have some guesses though. One possibility is that GNOME 3 (the window manager beneath Unity) is looking for the keyboard shortcuts in a different location than GNOME 2 (the previous window manager) was.
Unfortunately, when you click on the System Icon (little gear) in the top right corner, it will show that Lock Screen is mapped to Ctrl+Alt+L. I think this is a bug – the displayed shortcut seems to be hardcoded into the menu instead of being dynamically read from some configuration file (I could be wrong, but this is what I have observed the past few minutes testing scenarios for your issue).
Next, you can check to see what shows up in System Settings->Keyboard->Shortcuts->System for Lock Screen. The easiest way to access the Keyboard configuration is to type keyboard into Dash and select the app.
Select the Shortcuts tab. Then select System from the list int eh left hand side.
If it shows Lock Screen is mapped to Ctrl+Alt+L, then I would suggest mapping it to a different shortcut – say Ctrl+Alt+Shift+L.
Close the keyboard app and try out the new shortcut.
If it works, then I would open the keyboard app, remap the shortcut back to Ctrl+Alt+L and close the keyboard app and try it again.
If it works this time, it means that the upgrade from 11.10 -> 12.04 somehow missed your keyboard shortcut settings.
This is one of the problems I find with Linux, settings are stored all over the place and it is not always obvious which ones you are using. It could be (I am guessing) that at some point you had installed a different window manager in 11.10 to replace Unity and it had its own place to store keyboard shortcuts. When you upgraded to 12.04, it didn’t pick up those shortcuts.
Let me know how things work out because I am curious.
Thanks for your question.