unix and system commands not wainting fro complete output.

Hi, I am running a grep command on big file using both system and unix functions (without '&') inside a script. I have noticed that the script sometimes does not wait for the command to finish returning the grep's output, which in turn gives me errors later on as the expected output is cropped. It is almost as if it were a timeout on this function and depending on my computers load it just ignores the rest of the output although it still gives me a status 0, which means that it ran correctly.

Has anyone else had the same problem? Is there a way (without using pause) to tell matlab to really wait for that output to complete? Thanks