I noticed the bioluminescence at first, but it appeared as kind of odd that it lights up so much after 5 minutes, and I don't think it was like "lighting up" because the sun was gone, it was already full night before he lit the torch, the glow would be definitely more apparent imo.

Anyway, when I was in IMAX on Monday, I noticed something that is not on Blu-Ray. It's a rendering error just after the hometree collapsed. Somebody pointed it out with a screencap from the game on AF, but when I checked the BD it was alright. But IMAX has a higher screen so it was there. It's a moment when there is a view on the torn out base of hometree with smoke and debris falling of the roots, just before Quaritch says "tis a good work fellas". Watch the smoke on the top right, it kinda disappears at point where it's cut off on Blu-Ray lol.

That was the whole idea with it not being obvious until Jake notices it.
But here's a semi-scientific theory:
The ambient bio-luminescence is based on the light from the sun, it has a base level that is not as noticeable. When Jake lights the torch it is a more bright light that triggers the luminescence more. Bio-luminescence can be stored from light or ambient and always 'on'. It truly wasn't noticed because there wasn't as much light to trigger it until he lit the torch.