I ran into a particularly odd problem when I moved to Flash CS3. It no
longer allowed me to place batch files in the fscommand directory and call
them from a flash projector file. I found this article while searching for
a reason why, and it provides an excellent way to overcome the current issue
with Flash CS3 (and helps with the “flashing black dos boxes” that many
people have to work around when using batch files in fscommand).

http://www.northcode.com/blog.php/2007/08/07/Conquering-FSCommand-EXEC-Part-
1-Proxy

Basically, it provides a software proxy by which you can call out to those
Batch files from Flash projector files (and eliminate the DOS box at the
same time). Just download proxy.exe and rename to match the batch file you
want it to execute.

Example: Want to run “dosomething.bat” so you rename proxy.exe to be
“dosomething.exe”.
and in flash you would call it similarly: fscommand(“exec”,
“dosomething.exe”);