First question - is it possible the PLC is being powered down? There was a customer who was "setting up" the CPUs by powering them up, downloading the program, switching to RUN, then powering down. The ECOM100s write this data to FLASH, and that takes time. Each "write" IBox takes time, so they all have to finish.
It's possible to corrupt your ECOM when configuring them either through NetEdit or via IBox instructions if you power down the module/base in the middle of writing to it.
Looking at your logic, it looks like you are doing this with multiple ECOMs serially, which is okay - just make sure you are not powering down anytime during this sequence.
How often does Stage S1 get run - hopefully just once at power up?