On Windows, some information about the Maya 2011 File Browser and the Maya 2011 Color Picker is stored in the registry, not the userPrefs.mel file as you may expect.
For example, the position and size of the Maya File Browser are stored in the registry location: HKEY_CURRENT_USER\Software\Autodesk\Maya\2011.5-x64\FileDialog (depending on the version it could also be in 2011, 2011.5, 2011-x64).
The syntax of 'pos' is @Point(xxx yyy), as illustrated:
If the situation arises where you can't see the Maya 2011 File Browser, you would check the value of the FileDialog key 'pos'. Try resetting this value to @Point(0 0) and then restart Maya.
Thanks to Nicolas Holst for the tip.