After the 3dvolreg on the catenated runs, the images from run #2 should thenceforth be properly aligned to run #1 (from which the base image was drawn, I gather). If you time-animate the images after the 3dvolreg run, do you still see gross subject movement?
You can time-animate by
* pressing down the Time Index up-arrow button
* opening a graph viewer for the EPI time series and pressing the 'v' key when the mouse cursor focus is over the graph window
Zorkon the Volregimific