I am going to be making a change in Version 3.9.3 that might impact some users. I had once introduced a method to include custom PHP in the theme. That was more than 20 months back. Lots of things have changed since then, including provision of support for child themes.
If anyone is using that piece of functionality (and I doubt if the total count of such users is more than 10), I will be removing it in 3.9.3. Note that you can take all the functions defined in the Custom PHP file and put them in a child theme’s functions.php file.
Please feel free to post here in case you have any questions.