When I installed the mathStatica application, it seems to have made some kind of change deep in my Mathematica 8.0.4 system files. That change causes the mathStatica palette to appear out of alphabetical order in the Palettes menu. And the palette notebook does not set any value for MenuPosition.
In $UserBaseDirectory/Autoload/PacletManager/Configuration/FrontEnd/init.m I see:
SetOptions[$FrontEndSession,
PalettePath -> {ParentList, FrontEnd`FileName[{$UserBaseDirectory,
"Applications", "mathStatica", "FrontEnd", "Palettes"},
"PacletManager" -> True]} ....
(Note that on my Mac OS X 10.7.3 system, $UserBaseDirectory is the same as $BaseDirectory.)
However, if I delete the PalettePath option there, quit Mathematica, and restart it with clean preferences and clean cache, nonetheless:
that same
PalettePathoption reappears in the sameinit.m; and then of coursethe mathStatica palette appears again out of order in the menu
Paletteslist.
Question: what changes to some system file might cause this annoying and persistent behavior.
I've looked at all the init.m files I could find inside the Mathematica.app package (which is how the Mac bundles the entire $InstallationDirectory) but don't see anything suspicious.