There is a small plastic gear with a square hole in it under the lower assy that probably either has the square hole stripped in it or the teeth stripped off of it.
You have to take the press apart to fix this but even my 22yr old pro1000 came with an extra gear and I've never had to use it.
this gear, or the plastic larger gear it runs against are responsible for turning the indexing rod.
Take the turret out, raise the ram, and there is a screw under the carrier assy that secures the carrier to the ram, not the timing screw, loosen it, raise the ram, put two pieces of something the same size between the ram and the carrier and pull the ram back down. This will pull the ram out of the carrier so you can just lift the carrier assy out of the press. Turn the carrier assy over, take the two screws out of the cover over the gears and you will see the problem.
Almost always it is the small plastic gear with the square hole in it that the indexing rod runs through.
Replace the gear and reassemble. When you retime it the shell plate, hold against the direction it wants to turn and time it so the shell plate turns to it's correct position without allowing the ball and detent to click it into place.
This will insure correct alignment whether cycling the press fast or slow.