Probably you must to increase the AA sampling to reduce the flickering. Sometimes is not possible to remove it completely, and is necessary to apply a filter in post production (as Noise & Grain -> Remove Grain of After Effects).
This is a typical problem when rendering very detailed objects (as trees). You can find some useful posts about this issue here (both for VRay and Mental Ray):http://www.itoosoft.com/forum/index.php?topic=905.msg3048#msg3048
2 - I've tried to bake my 1350 frames animation with an interval render of 50 frames, in that phase the renders take about 5 minutes per frame. When i start to render the full animation, loading the previous saved *.vrmap file, the renders take about 10 minutes per frame. Any clue?
Are they stored locally or in a network share ?
Anyway, i would suggest you post this question in the VRay forum as well. They have more experience with these type of problems. If that helps, Forest doesn't modify or has access directly to the GI files, so in this case, this seems a purely VRay issue.