Hi Mark,
It is hard to say the exact reason. Those Sitara boards often need a lot initialization to get it in the correct state before loading and running the program and if you want to reload or load another program, you may need to redo that initialization that is done by the startup GEL file. It is a fairly common scenario. You can try looking in the device forum, the experts there can probably give you a better explanation as they will be more familiar with the initialization needed for the device/board
ki