You are probably running it as a NSP. Run the NRO, change the settings, then use b-button exit to exit the app. Pressing the home button to exit, or running it as a NSP means that it will never save the changes.
Same bug as 1.0 for me. I delete "Switch/sx" folder on the sd card before copy new 1.1.
SD (exfat) --> 5 .xci files (all in the same directory /sxos/xci)
SX OS .xci Loader --> 5 xci (I can mount and use all of them without problem)
SX Installer xci menu --> only 2 .xci
SX Installer file browser menu --> 5 xci (I can mount and use all of them without problem)