you definitely need to do a complete flash...rootfs+EMMC, both .bins...otherwise the problems will continue..
I had the same situation up until yesterday, the Mail app absolutely didn't work, though I had the accounts properly set and visible in Accounts app...my gallery was all empty, though I could see all my pictures in Pictures folder in Filebox...reboots didn't help, resetting or clearing the phone neither...I reinstalled FW via NSU, no change whatsoever...
I must add that this hassle had started when I was playing with speed up transitions in QuickTweak app..that was crucial mistake as I then chatted with Schturman, who made the app...until it's ready for PR1.2, stay totally out of it...
also, backing up the phone is kinda problematic as neither in-phone backup, nor Nokia Link's one did good for me...anytime I restored, even after hard flash, the phone was messy again...
so I suggest to fill up the phone with apps, accounts and other stuff without any restore, as a clear device...it'll definitely help...
to be honest, I'm too rather disappointed with Nokia's approach at this update as it clearly has a lot of bugs and some tricky issues appear at almost every owner...it's really exhausting just spending time with flashing and reinstalling...
nevertheless, after all this my phone works pretty good and I'm kinda satisfied with the speed and stuff...only some apps act strange, Shortcuts don't work at all, Gtalk video call totally lagged it so I uninstalled it...