I noticed that in my most recent copy of SPM5 and its updates, many
toolboxes were adding themselves to the matlab path after I started SPM and
pushed the "fMRI" button. (Equivalently, after I started SPM by typing spm
('fmri') in matlab.)
For a toolbox named "X", the line that caused this was in the file
.../toolbox/X/spm_config_x.m
and the line is of the form
addpath(fullfile(spm('dir'),'toolbox','X'));
My impression is that that line shouldn't be there, and it seems that that's the
line that puts the toolboxes in the matlab path even before any toolbox has
been selected using the menu on the main SPM5 window.
