Success! sort-of...
I got my Sapphire today, mfg date: 08/12. With Command 2.0.0.0 (via "W"->Help->About), I initially couldn't extract from the Sapphire. It would go through the motions but at the last minute, it would complain about "Some kind of exception occurred" and Command would abruptly quit.
I jumped on Whelen's Website and noticed they put up "CenCom Sapphire 1" and "CenCom Saphire 3" since I last took a look.
I had no luck extracting from the Sapphire with "CenCom Saphire 1"...so I moved on to version "3".
I'm pretty sure I did _not_ perfectly retrace your steps...but
1. In "Command", I tried changing the pattern and phasing to SF60 and in my case, the heads all stay on the same phase...sometimes 180, sometime 0.
2. Good news: Using "CenCom Saphire 3", while I had some troubles installing it, I was eventually able to (somewhat) smoothly extract the original config on the Sapphire, make pattern and phase changes, transfer them back down to the Sapphire, and observe expected behavior.
Bottom line: you might have some luck with "CenCom Saphire 3" available here:
https://www.whelen.com/software-downloads/