After reading through the help file, I can't determine how setting the AUTO Program to retentive would solve the issue.
Retentiveness is a design decision. Assuming after a power cycle (or PGM->RUN transition), all the control memory should be OFF (by design), then you are correct. But if after a slight power glitch, you expect your machine to run where it left off, keep everything retentive. It appears even a slight power glitch you expect everything to be OFF (i.e. just about everything needs to be non-retentive).
It's the C bits that also need to be non-retentive, i.e. they need to turn OFF after a power cycle or PGM->RUN transition. Realize that with the AUTO program NOT running after a power cycle, its logic CANNOT turn the C bits OFF (or ON) - they will just be in their retentive state after a power cycle. Hence, why C bits probably need to be non-retentive. It's the same as an unused retentive C-bit - it will be OFF or it will be ON after a power cycle - there is no logic driving it ON or OFF, the retentive value just "is". Just make most things non-retentive (i.e. go to a state of 0) after a power-cycle or PGM->RUN transition.