Have You Tried this? 
 
Added program execution after transfer complete. 
To use this functionality you must add the following section to the FlashFXP.ini 
[run] 
app=<full\path\to\exe> 
param=<any params you need to pass, use the %f macro to pass the filename> 
show=1 
show application window has two values 0=hidden 1=visible 
 
Simple Example 
[run] 
app="c:\vscan.exe" 
param="/scan %f" 
show=0 
		 
		
		
		
		
		
		
		
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