Rebuilding InDesign Preferences
Preference files for applications can become corrupt without warning: They hire their relatives for high-paying jobs they're not the least qualified for, they bribe judges, plant evidence, hide ill-gotten gains in unnumbered offshore accounts, steal candy from babies and make your mama cry.
Or they just make your program act strangely.
The fix is to replace the bad, bad preferences file with a fresh new one. It's the first line of defense when trying to solve an intermittent and often random problem that appears to affect all the documents a program works with. If an application can't find an existing preference file, it builds a new one with factory defaults when it starts up, so simply deleting an existing preference file and restarting the program is usually enough to do the job.
[June 1 2010: I have updated this post so instructions apply to versions CS2 to CS5. -- AM] The fastest way to do this for InDesign, InCopy, or any other program in the Creative Suite is to quit the program, then hold down the Command-Option-Shift-Ctrl keys (on Windows, hold down Control-Alt-Shift) while you start the program up again. You may need to choose "Open" from the program's contextual menu to get the program to boot up because you're holding down modifier keys, but you'll figure it out.
While the program starts up, keep the keys held down until the splash screen appears along with an alert offering to "Delete InDesign Preferences File?". Release the keys and click Yes. InDesign will complete the boot-up process with fresh, clean Preferences to replace the sick one it just deleted. Test the program ... chances are, the problem you were suffering is now history. That's all, nice and simple!
When you rebuild preferences, you lose any custom application defaults you might have made in the Preferences dialog box, and any Presets you created (custom PDF presets, Document presets, etc.). Also, in early versions of InDesign you lose custom Glyph sets - poof, they're gone. So, when your InDesign preferences are healthy again, back up the actual "InDesign Defaults" file (see below) for safekeeping. That way, the next time you need to rebuild sickly InDesign preferences (and there will be a next time), you could replace the generic InDesign Defaults file with your healthy backup containing your custom settings.
The good news is that some application-wide settings you might have added (as opposed to modified) do survive the rebuilding process. These include custom Workspaces, saved Find/Change queries, keyboard shortcut sets, words you've added to AutoCorrect, and custom dictionaries. Also, scripts and plug-ins you might have installed aren't part of the program's preferences, so those will always remain intact.
Where are the InDesign Preferences files stored?
In Macintosh OS X and Windows, each user of the computer has their own user account; so Preferences are stored in that user's own set of application preferences. Technically, by the way, the file is called "InDesign Defaults" (not InDesign Preferences).
On a Mac, start at your Home folder, and go to:
[Home] > Library > Preferences > Adobe InDesign > version > language > InDesign Defaults
C:\Documents and Settings\<USER>\Application Data\Adobe\InDesign\version\language\InDesign Defaults
Windows Vista or Windows 7:
C:\Users\<USER>\AppData\Roaming\Adobe\InDesign\version\language\ InDesign Defaults
"Version," of course, means whatever version of InDesign you're using. You'll find a version folder for every version of InDesign you've ever installed on that computer. Version 3.0 = CS1, version 4.0 = CS2, version 5.0 = CS3, version 6.0 = CS4, and version 7.0 = CS5.
"Language" is your computer's default language, such as "en_US" for US English. The language subfolder was added to the InDesign preferences path starting with version 6 (CS4)
Along with the InDesign Defaults file you'll find a whole mess of files. The ones that get rebuilt if you hold down the magic keys at start-up are, as far as I can tell:
FindChangeData [starting with CS4 this file was moved elsewhere, see below]
InDesign ClipboardScrap [ditto]
InDesign DragDropScrap [ditto]
InDesign OSXServicesScrap (Mac only) [ditto]
InDesign Recovery [ditto]
InDesign Saved Data [ditto]
Please don't ask me what each of these do, I have only a vague idea. But I can tell you that when I delete my own Preferences (instead of having InDesign do it for me), I just trash the InDesign Defaults file, restart InDesign, and that usually brings InDesign back to health again.
More Preferences Tips
If InDesign freezes up or quits while you have documents open, the next time you start up the program you'll see those documents re-open, like Lazarus back from the dead, very often with unsaved-changes intact. Woo-hoo! Save those suckers immediately (after giving them a once-over), they're in a fragile state. You might want to save them with a different name in case you have to go back to the "good" saved file on your hard drive.
These zombie documents were created because InDesign had versions of them in its InDesign Recovery folder, also located in your user account's settings files on your hard drive. If you're using InDesign CS1, CS2, or CS3, you'll find the recovery files in the same location as InDesign Defaults, as explained above.
In CS4 and later, these important files were moved to a different location:
Macintosh OS X:
[Home] > Library > Caches > Adobe InDesign > version > language > InDesign Recovery >
C:\Documents and Settings\<USER>\Local Settings\Application Data\Adobe\InDesign\version\language\Caches\InDesign Recovery\
Windows Vista or Windows 7:
On occasion I've had a document get damaged enough that when InDesign starts up again, as it's attempting to open the recovery file, it throws up its hands in disgust (I always imagine two little Hand tools waving in the air) at the mess I've made and immediately quits.
When that happens, I hie myself over to the Preferences or Caches folder for my version of InDesign and delete both the InDesign Saved Data file and the InDesign Recovery folder (including any files inside it). In most cases I can start up again with no problems, open the last officially saved version of my problem child layout, and keep working. (Though I'd probably export it to .inx or .idml and re-open it, saving it with a new name, to clear out any document corruption that might have contributed to the issue.)
Finally, if all else fails, try this: Drag that entire InDesign Preferences and Cache folders to your desktop and then start InDesign again. It will recreate the folders it needs and their myriad files. I say "drag them to the desktop" instead of deleting because you might have finely-tuned workspaces or long lists of AutoCorrect entries that you'd like to hang on to.
So if deleting the folder puts InDesign back in the pink again, you can try bringing over a Workspace xml file or two at a time from those precious subfolders in your old Version n.0 folder to their homes in the new one, testing InDesign all the time to make sure everything's okay before bringing over the rest.
And then ... when everything's working great ... back it up! I keep a copy of my entire, healthy, customized Version n.0 folder (renamed My Version n.0 - backup) at the same level as the real one (don't worry, InDesign sees the strange folder name and ignores it), so I always know where to find my healthy prefs.