Fix for System Preferences Keyboard Shortcuts crash

Question

This is not a question, but a solution to a problem that proved difficult to identify and fix for me and three Apple Support personnel, so I thought I should post it here in case others encounter the same issue. I spent a lot of time searching the web and Apple Discussions for this and related issues did not come up with any solutions.
After migrating from Snow Leopard on 2009 MacBook Pro to Yosemite on a new MBP using the Migration Assistant, things went surprisingly smoothly for the most part, until I opened the Keyboard pane of System Preferences. Then, clicking on the Shortcuts tab immediately caused System Preferences to crash, reproducibly.
Crash Reporter pointed loosely to a keyboard-related preference setting. But "com.apple.preference.keyboard" is the name of an OS process, not a .plist file. I searched the web to try to find out where Keyboard Shortcut settings are stored in Yosemite, and also for a possible way to reset the settings to default in Terminal (e.g. using the "defaults" routine), without success. (Apple Support was not happy that I had Terminal open when they shared my screen, and seemed never to have heard of this routine).
Process:               System Preferences [948]
Application Specific Information:
objc_msgSend() selector name: retain
com.apple.preference.keyboard v.14.0 (Keyboard)
objc[948]: GC: forcing GC OFF because OBJC_DISABLE_GC is set
Repairing disk permissions, rebooting in Safe Mode, zapping the PRAM, and trashing ~/Library/Preferences/com.apple.systempreferences, some keyboard-related .plist files, and the system prefs and International prefs caches did not fix the problem. With Apple Support, we isolated the problem to my user account, as the same crash did not occur in a test account, or in another account migrated at the same time. Nevertheless, Apple's techs had me removing various menu items and programs also running in these accounts that I had deactivated (Sophos AntiVirus, Little Snitch, etc), and downloading and reinstalling Yosemite, which seemed unlikely to address the cause, given that my main user account was the only one affected.
Apple never had me check 3rd party preference panes (which I should have thought to do earlier myself). Opening and closing an older version of Default App ((RCDefaultApp 2.0.1), a free 3rd party utility, in the Preferences pane, transiently solved the problem. However, it recurred on removing it, and was not fixed by installing the latest release of this preference pane, nor did removing three other 3rd party preferences panes (MacFUSE, a Citrix app, and Flash Player).
Finally I went back to ~/Library/Preferences and looked for any files that had been modified around the time the problem transiently disappeared, and stumbled upon com.apple.symbolichotkeys.plist. After viewing its contents with Property List Editor and finding this article, I thought that this file was likely the problem.
I logged into my root account, verified that Shortcuts worked fine there, and that this file changed with a change in Shortcut settings, and (after renaming the offender to save it as a backup), replaced the file in my main user account with a copy of the one from the root account.
I repaired permissions in the offending account, rebooted, and voilà - problem solved!
NB If you are in a similar situation, before trying this fix (at your own risk!), I strongly advise backing up your computer first, and saving a copy of the presumed offending file in case you have to put it back because of unforeseen consequences. You do not need to enable and use the root account; instead you could log in to a new administrator account, or another user account, verify that Shortcuts works fine there (it would not be a bad idea to set up any user-defined App Shortcuts you want there); and copy the file to a shared folder.
Then switch back into the offending account, go to your user Library/Preferences folder (~/Library/Preferences using Go To Folder in Finder), and replace com.apple.symbolichotkeys.plist in that account with the one from the shared folder. You should then repair disk permissions afterwards and restart.
If it works, Shortcuts should open fine. Be sure to check each category  in the left-hand panel of the Shortcuts panel (e.g. LaunchPad & Dock, Mission Control, etc.) for conflicts, and resolve those by disabling the offending duplicate key combination assignments (I had two, marked by yellow triangle alerts).

Answer 1

Ward Clark wrote:
Thanks, V.K., for your comments.
I wrote: Enter is accepted, but it's treated the same as Return
not for me. it's both displayed and treated differently. I suspect what you are seeing is a byproduct of using a haxie such as Menu Master.
no it's not. it's treated differently.
In Leopard, Menu Master let me assign Command+Enter to Address Book > Edit Card. When I attempt the same using Keyboard Shortcuts, both Command+Return and Command+Enter are displayed as Command plus a "return arrow." After that, in Address Book, both Command+Return and Command+Enter invoke the "Edit Card" menu action.
not for me.
if you want to use those keys in the shortcuts use one of the many 3rd party app launchers. any one of them will let you do this: Qucisilver, Butler, Spark, Launchbar, ikeys, quickeys etc.
I've been using QuicKeys since the beginning of time, and I have some experience with Butler and LaunchBar. They're useful for what they do. But, as far as I know, none add keyboard shortcuts that are displayed directly in the menus. That display feature is what makes Menu Master and Systems Prefs > Keyboard Shortcuts so attractive.
that's because Menu Master is a haxie. none of the other programs mentioned are. you want such functionality you are going have to use a haxie. personally - i stay away from them as they destabilize the system.
When I'm considering new shortcuts, I use KeyCue to display all current shortcuts in a single display. KeyCue now displays QuicKeys shortcuts in the same display, which is a big help.
-- Ward