Just won't stick...
I have a really weird issue. Let me say the rom is freaking gorgeous and FAST. I'm sure the problem is on my end and not with the rom.
I started by completely repartitioning my 32 gb sd card as per instructions earlier in the thread. I then wiped everything I could find. I'm using Amon. No matter how many times I check off several Quick Setting items to be hidden they never actually get hidden. I have also checked off to hide the GPS icon and it goes away briefly but then pops up again after a reboot. And finally I have the problems with changing the lockscreen shortcuts. Despite all of this I will not give up on this rom. I have never seen such a fine piece of work. It's really impressive.
Update: Bizarre... I also repartitioned my stock SD card, reloaded rom with stock theme, etc. and have the same exact issues. It has to be hardware related. I'm still gonna keep using it. This rom is just too cool to give up on.