Calling R from Matlab inside parpool

Hi! I have a code where I call R from Matlab, do some calculations and retrieve back the information to Matlab. The information is exchanged through CSV files. There are several iterations in the code. The code works fine in serial mode. But when I use parpool it seem to disrupt the information in the CSV file (for example I am supposed to get a 120-by-3 table at each iteration ,but in some iterations it creates a 125-by-3 table). Is there a solution for this?

Thanks.