I was having this same issue and found the source of the error on my machine:
Try running the command "savepath" from the command line rather than from the Matlab "Set Path" option.
For me, this showed that the built-in function "isdir" was replaced by some File Exchange code that I was using, and that code had an error. After removing those files, "savepath" was able to use the correct "isdir", and I was able to save the path again. After this fix, saving the path worked both from the command line and using the "Set Path" dialogs.