Apps will sometimes not launch

Question

Hi.
Since Thursday (26th September) my 2011 MacBook Pro has been acting strangely.
Most of the time, all seems okay, but on Thursday, yesterday and again this afternoon, it seems to go into a sort of 'spasm', and refuses to launch any apps at all.
When this happens the app's dock icon just keeps bouncing in my dock, for about two or three minutes, and then when it stops bouncing there is no sign of the app's window anywhere on the screen and there is no little light below it on the dock shelf. If I click the dock icon again, it doesn't even start bouncing. Just nothing at all.
Once the computer goes into this 'state', it will not launch any Mac apps at all, either from the dock, from the apps folder or by double-clicking a file anywhere. I can't even open the System Prefs window to see what's happening.
Curiously though, (and rather annoyingly...), all my Windows programs still open and run perfectly normally under Parallels.
I cannot restart or shut down my computer via the Apple menu, because when I try to nothing happens, and so I find myself having to do a 'forced shutdown' by pressing in and holding down the physical power button on the computer. Once I've shut it down and restarted it, all seems normal again. Until it happens again.
All this is getting very irritating.
As I say, it started happening on 26th, and I updated to OS X 10.8.5 on the 25th. Could there be a connection? Is anyone else having similar problems?

Answer 1

Back up all data. Don't continue unless you're sure you can restore from a backup, even if you're unable to log in.
This procedure will unlock all your user files (not system files) and reset their ownership and access-control lists to the default. If you've set special values for those attributes on any of your files, they will be reverted. In that case, either stop here, or be prepared to recreate the settings if necessary. Do so only after verifying that those settings didn't cause the problem. If none of this is meaningful to you, you don't need to worry about it.
Step 1
If you have more than one user account, and the one in question is not an administrator account, then temporarily promote it to administrator status in the Users & Groups preference pane. To do that, unlock the preference pane using the credentials of an administrator, check the box marked Allow user to administer this computer, then reboot. You can demote the problem account back to standard status when this step has been completed.
Enter the following command in the Terminal window in the same way as before (triple-click, copy, and paste):
{ sudo chflags -R nouchg,nouappnd ~ $TMPDIR.. ; sudo chown -R $UID:staff ~ $_ ; sudo chmod -R u+rwX ~ $_ ; chmod -R -N ~ $_ ; } 2> /dev/null
This time you'll be prompted for your login password, which won't be displayed when you type it. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
The command will take a noticeable amount of time to run. Wait for a new line ending in a dollar sign (“$”) to appear, then quit Terminal.
Step 2 (optional)
Take this step only if you have trouble with Step 1 or if it doesn't solve the problem.
Boot into Recovery. When the OS X Utilities screen appears, select
Utilities ▹ Terminal
from the menu bar. A Terminal window will open.
In the Terminal window, type this:
res
Press the tab key. The partial command you typed will automatically be completed to this:
resetpassword
Press return. A Reset Password window will open. You’re not  going to reset a password.
Select your boot volume ("Macintosh HD," unless you gave it a different name) if not already selected.
Select your username from the menu labeled Select the user account if not already selected.
Under Reset Home Directory Permissions and ACLs, click the Reset button.
Select
 ▹ Restart
from the menu bar.