it's normal.
Exiting the settings application always reboots the consoles, so it exits and reset any memory hacks and patches the consoles has. You are back to a clean version of the menu.
That's also why you should be very careful if you want to update your emuNAND. If you want to update, NEVER exit the settings. open the settings, and go to update. if you exit, it will reboot and you will update your sysNAND, losing softmod capability.
before updating your EmuNAND, ask here to be sure you are using the proper method for your version. don't just assume randomly found tutorial is good.
Palantine CFW is one of the first and old CFW released. there are a
lot of different CFWs, you don't "install them with Rx", they are different softmods.
rxTool is more recent and can do more things than palantine.
I think the most recent CFW are : rxTool, Cake CFW, ReiNAND and NTR v3
others are older, even if still functional on their respective required system version.