This behavior can occur if the MCR cache becomes corrupted in between two executions. To resolve this issue, you would need to delete the directory to which the CTF is extracted, so that it would be re-extracted with the next run of the standalone application. This directory can be obtained by typing the following at the MATLAB Command line:
mcrcachedir
In version MATLAB 7.6 (R2008a), this defaults to a sub-directory of your local settings directory on a Windows platform. In versions MATLAB 7.7 (R2008b) and higher this defaults to the temporary directory as specified by the TEMP environment variable. These directories may be modified when running automatic updates or running backups as configured by your system administrator.
Also, to avoid these sort of directory corruptions, make sure that no other process can reach the directory to which the CTF gets extracted.
