Maybe related?

http://feedback.arma3.com/view.php?id=22876

@gruso:
Hi,
can you please compress and upload Launcher's log files from affected machine. Logs can be found in your user profile:

C:\Users\<username>\AppData\Local\Arma 3 Launcher\Logs

Also it would be helpful if you could upload your preset files:

   C:\Users\<username>\AppData\Local\Arma 3 Launcher\Presets

@Chairborne:
It's not related. "Command Line" is not persisted by design.

BIS Wizard, I fear I have wasted your time. Breaking my issue into two parts:

1. Command line options. After reading Chairborne's ticket, I realised the parameters kept returning in the Launcher because they were present in Launch Options in the Steam client. Colour me embarrassed.

2. Mod groups. It appears that these are now working and being saved as expected. This was after deleting all the folders mentioned in my original report. So although the issue _was_ present beforehand, I have now deleted all the evidence (including efficiently emptying the recycle bin).

I have attached the logs and profiles as requested, but they're only going to show situation normal now.

Thanks for your time, and sorry I was unable to give you the logs you needed!

I like this guy.