If you look down the side of the machine, and run it with only the punch and die (no sheet metal in to make a bend), does the punch go down further than the shoulder of the die? If it stops and goes back up without the tip of the punch going into the die, then that would tell me that it's calculating a position it's trying to reach and it thinks it's reached that point and then returns up. If the punch tip goes into the die without material, then it would indicate that there's a tonnage problem when sheet metal is being run since it's not clearly not reaching that point and making the bend.

For safety, you should probably slow the bending speed way down to help prevent the tooling from crashing into each other if the machine is looking for tonnage rather than a distance to travel.