Hi Ben
Searching for something else I came across your post. You have probably resolved the issue now, but my understanding is that if you transport a process chain with the start variant set to Direct Scheduling>Immediate Start it will run as soon as it is active in the target system.
To overcome this, I transport all my process chains with the start variant set to Start Using Meta Chain or API. Once the PC is active in the target system I change the start variant to the required Scheduling Option.
Regards
Sean