Use the Event Server Monitor tool to see what runs when. Also check to see how long these FTPs take. By setting up the runs, to limit the number of maps running, you might also reduce network traffic and speed things up that way too. If, by running every 5 minutes you get conflicts, it might be possible to set some of the maps to run at a slower rate. Rather than stagger the start time, you can stagger the run time by setting the trigger time variables.
On a test box, see which map uses the most CPU. It should not be the FTP map, but the one that does the actual processing. The problem could also be that the FTP maps are using all the threads, and there are not enough to run the other maps, so you get into an init pending situation. The server might need more CPUs, or you may need more than one server.
BocaBurger
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The pen is mightier than the sword, but the sword hurts more!