I just upgraded to R2015a on Windows 8.1 Pro x64. I set Matlab's initial folder to "C:\Users\Alex\Documents\MATLAB" in the GUI. I verified it's set by executing userpath.
I then added a few custom folders to path using addpath c:\code\foo c:\code\bar. Launching pathtool does show indeed the custom folders on top, and executing functions from those folders works.
I then saved the current path definitions from the pathtool GUI, which creates pathdef.m inside "C:\Users\MYNAME\Documents\MATLAB\pathdef.m". I verified that pathdef.m does indeed contain c:\code\foo and c:\code\bar
However, upon starting Matlab, my custom folders are no longer in the path. It's always reset to the default set of dirs.
The exact same procedure in R2014b works just fine, but not in R2015a. Any clues?
p.s. I don't want to edit files in MATLAB\R2015a\toolboxes\local. As a workaround right now I created a file C:\Users\Alex\Documents\MATLAB\startup.m where I call path(pathdef); which does what Matlab is supposed to do upon startup ...