I would say it is almost certianly that the script is setting a speed limit on the sends, something mirc allows to be done.

However one other thing i have seen , is if you have a fast send 100's of K a second and your script is often processing things, so is momentarly delayed, the sending of files are not on a sperate thread, so untell the script completes what ever it might be doing, any continuing of the send is paused, assume that the script might have a ON TEXT and its an active channel say 3 lines a second, and each line takes .1 second to process (not unfair to say if its xdccklipper running on a slower machine), then for .3 of a second there can be no send, this sometimes well mean there is a delay before the next block of data is sent, maybe reducing a send from say 150K/s to 120K/s, the smaller the send size the harder it is to see any change of course.
This however would effect sends manually started if the script was running, Im not sure by your message if u ment his manual sends went fatser than his scripted sends that were going at the same time, or if u ment if he doesnt have the script installed his sends are faster.