ShapeShifter can't find the Finder

"ShapeShifter won't theme Finder"
"ShapeShifter preferences reset"
"ShapeShifter not applying to Finder"

Frustrating as it can be, this problem for many can be a forehead slap once fixed, and fits perfectly into the Bum Scoop Rescue objective of answering the often asked and rarely answered questions.

So you've just updated something somewhere in OS X and ShapeShifter no longer themes Finder and/or other Apple applications.

If you've started searching you've probably already gone through all kinds of file dumps, though we will go over those steps later, if this simple first step doesn't fix everything.

1. Are you up to date?
Always, always make sure you've started with the simple things first. Make sure that both ShapeShifter and Application Enhancer are up to date. Go ahead and just use google to get to Unsanity's download pages and grab the latest installers for each of these and run them. Restart your computer, and most likely everything will be fine. The problem on this machine occurred after a Quicktime update, and it was found that 2.0.3 of Application Enhancer was installed, and the latest version available was 2.5. Needless to say there was a large gap in fixes that were the key to fixing this problem.

2. Not so easy? Don't worry.
If updating didn't fix the problem, or you were up to date, not to worry, it should still be a simple fix. Bring up the ShapeShifter preference pane and hit restore defaults under the "Apply" tab. This restores the aqua theme, quit system preferences once this is done. Go ahead and open a new finder window or hit CMD-F and start searching for anything containing "shapeshifter" in the name. What we're looking for are any files that end in ".plist". These are preference files and must be deleted to bring ShapeShifter back to it's starting state.
NOTE: This will unregister your copy of ShapeShifter, so make sure you have your password, activation code, and name handy to re-register it once this is done.
Now search for "finder," again looking for a file that ends in ".plist". It should be located in /Users/[YOURUSER]/Library/Preferences, once you find it, delete it. Now restart the computer and see what's what.

3. No luck?
Once you've double checked that all of your Unsanity installations are up to date, and have deleted the preference files, you still have applications that refuse to be themed you're going to have some deeper OS X troubles going on. It also can't hurt to check that you're running the latest version of OS X itself, though that shouldn't usually affect things.