Finally sent my phone back to sony for repair, first repair, on inspection at the counter, found 3 dead pixels, so they had to send it back for repair again. It is back with me now, but I'm still experiencing the same issues on the latest stock rom and the panel looks slightly different from the one I had before (light and proximity sensors can be seen, easier to see transistors under screen in sunlight..) do they have different versions of panels?
Phones That I Own(ed):
Sony Xperia Z1 (C6903) --- PAC-ROM, bootloader unlocked --- main phone
Sony Xperia Z (C6603) --- Sent back to sony
Motorola Droid Razr (xt910) --- AOKP JB KeXeC --- dagger/backup phone
Motorola Backflip (mb300) --- CM7.2 --- other backup phone