file closing timing problem

Hello,
I hope someone can help me with what seems like a simple problem.  I  
have the following code:
system("swat_edit.exe", wait=FALSE, invisible=FALSE)
system("swat2005.exe")
In the first line, swat_edit.exe edits hundreds of input files, which  
are then to be used by swat2005.exe in its calculations.  The problem is  
that before swat_edit.exe finishes editing and closing all the input  
files, swat2005.exe begins, and an error occurs that such-and-such an  
input file is already in use so that swat2005.exe cannot run.
Naturally, one would think that changing wait=FALSE ot wait=TRUE might  
solve the problem.  But wait = TRUE gives an error.
I am using Windows 7 and Windows XP, and this problem occurs with both.   
I've inserted a time-delaying statement, z<- mean(runif(30000000,0,1),  
to buy time, but this only helps on the older computer I have, not on  
the new Core i7, which I really want to make use of.  The suggestion has  
been made to switch to a Linux system, but I'm having trouble getting  
the source code for swat_edit.exe so that I can recompile for Linux.   
Any ideas, if I want to try to achieve this in Windows?
Your help would be much appreciated.
John Joseph

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