Yeah I could not understand why FTB disabled this, it's not like it did any harm with it enabled, but anyway locate the minecraft\config\powercrystals\minefactoryreloaded\common.cfg file (on server for SMP) and change the below to true in the General section:
# Whether or not to generate rubber trees during map generation
B:WorldGen.RubberTree=false
Any new chunks generated should have the trees.