I just came across this little Maya oddity and solution.  I thought I would share it.

When you first launch Maya, you see the following message in the feedback box at the bottom of your workspace…

Error: Warning: Not all preferences were saved. See Script Editor for details.

Description:

Maya doesn’t retain any changes you have made to your workspace, such as which shelf you last had open, which panel set you were last using, or any other customizations to the interface in general.

Solution (Windows XP Pro, SP 2):

Create a System Variable called MAYA_APP_DIR and enter the path to the maya folder as it is in your “My Documents” target folder.

Here’s how:

1.Right click on ‘My Computer’ and choose ‘Properties’
2. Select the ‘Advanced’ tab, and click on ‘Environment Varibales’

3. Under ‘System Variables’ click on ‘New’ and name it: MAYA_APP_DIR. Set the value to the location you wish to use, e.g. D:/maya

4. Click OK until all dialogs are closed.

5. Restart Maya if you have it open.

Why does this happen?

If you change the target folder for your “My Documents” folder to something different since you installed Maya, this problem will occur.