This is possible because the matlabrc file on the machine where the executable was compiled might have modified settings (or a custom startup file).
MATLAB compiler when compiling picks up these (startup files). When the deployed application is run, it again tries to execute these startup file, but will throw up warnings if the path is not present.
Because of this reason, I'd recommend using the isdeployed (and ismcc) function to customize matlab start up routines.
if (~isdeployed || ~ismcc)
% Custom path additions, if not a deployed application or mcc
addpath(...);
end
