somehow you need to get the frames registered to one another.
if you dump the R, G, B into BPP together, they will all be registered to the reference frame you choose.
if you did BPP 3 times with 3 different references, then you'll have to pick one of the masters as a reference and align the other two channels to that master.
the LRGB combination tool (or ChannelCombination, or PixelMath - all of which can be used to create an RGB image from 3 masters) will not align anything; they expect that the images will already be aligned.
rob