New MATLAB R2015b has huge overheads when calling script files?

I have a function that calls matlab script (not function!) inside it. I found that in this case R2015b is 10–40% slower comapring to R2015a. The problem is in the lines when the script files are called. The profiler shows interesting results: the line

my_script

takes 59 seconds, while the script itself (my_script.m) takes only 23 seconds to execute. (R2015a shows adequate results: 27 and 26 seconds for the code line and the script itself)

I guess the problem is with the new JIT. Is it not a good practice anymore to use scripts?

[Walter Roberson]

It has been close to a decade since it was good programming practice to use scripts in MATLAB.

[Dmitry]

If I am not mistaken, until the recent release the overheads in functions were high (comparing to scripts). This is the reason I used scripts in low-level computation-intensive parts of the code.

[Guillaume]

I believe it's been the other way around for a while. There's no (or little) JIT optimisation in scripts, and full optimisation for functions.