Here's how its been:
Went to the Apple Store, they did a reset with their computers and eveything, Since I didn't have my computer with me I kept it around 3 hours in a "like new" condition, but I took over 500 photos with flash and it worked. I couldn't replicate the problem. I thought eveything was finally going to work.
I got home, restored it from my past iphone (as every generation of iphone I've had) and within 30-40 minutes it started taking the dark photos again!!! I then thought: "ok, maybe it's the restore, that some files are corrupted or something". So I reset it to factory settings, and added my apps and music like a new phone, no restore.
It was working perfectly for almost a day. And suddenly half an hour ago, it started again. Oh my.... I'm on my way back to the Apple Store. Hopefully I get a replacement and the new one works fine, though I still think it may be something to do with something I get in the phone: maybe a corrupted song, or an app that creates conflict. Anything.