Alright so just in case some one has the same problem, here is what happened:
I overhauled the drive train, the BB is a sealed cartridge so no maintenance possible other than cleaning the treads and putting grease to prevent rust. The BB had some corrosion on it but none could be found elsewhere. I inspected the frame with a light and every thing seemed good, no cracks, no corrosion. Looked flawless. Since I couldn't do anything else than buy a new BB cartridge in case the problem was still present I decided to re-install everything. I tried to reproduce the noise on the stand and was unable. I took it for a ride and I wasn't able to reproduce the noise again. The front derailleur needs some adjustment (chain makes contact). I will look into that, take it for a longer ride and pray that the problem went away.
I was careful to put a lot of pressure when tightening the BB and crankset. It's entirely possible it wasn't tight enough despite being VERY tight! The grease might have helped putting extra pressure on the BB or Crankset.
Thanks all for your answers and help!
