I'm still not able to reproduce this bug. I'm not sure what is different with my setup.

I've created an empty world with no mods. Built a small platform and only added a reactor, programming block, timer, and large cargo container. I filled the cargo container with two grinders. The timer is setup to run the programming block and then trigger itself again, with a one second delay. I loaded the Cargo Manager Script into the programming block. When I start the timer block, the grinders don't duplicate.

I then added some cobalt ore into the cargo container, split it into two stacks, and it gets recombined. This tells me that the script is running.

Is there something else I can try? Could another mod be interfering with the script?

No I was only using your script at the moment. Maybe It's just my game.

Well tried it again and nothing happend. Guess it was my fault.

Weird. Definately let me know stumble upon it again. I can't test everything so I appreciate you bringing it up anyway!