The first time you run, it has to break out the CTF archive as well as everything else.
Each time you run it has to check the md5 or equivalent to the archives to validate them, and then start executing.
The execution process involves the same amount of initialization as starting up matlab itself.
MATLAB Compiler does not compile to machine code: it just preparses the code the same way that is done the first time in a session that matlab encounters the file. The actual execution of the parsed code is by the same execution engine used by interactive matlab.
Do not use MATLAB Compiler to speed up execution: the speed will be the same.
If you want to speed up execution of code you should use MATLAB Coder
If you have a compiled execute and you need faster startup then have a look at Production Server