The ability to automatically clean up the mcrcache is not available in the MATLAB Compiler.
To work around this issue, you can create a small BAT file that can set up the environment, run the exe and then clean up afterwards.
@echo off
cls
set MCR_CACHE_ROOT=C:\Temp
Start complete path to your exe
pause
rm -r C:\Temp\mcrCache7*
Caveat: If you do this though, I think that subsequent runs of your program might take longer to launch because all the files in the CTF will have to be unpacked and recreated, whereas if you left them it wouldn't have to do that all over again.
