Well, I'm still not 100% sure of the cause, but I've managed to solve the problem of reduced bass. Took a while for it to occur to me, but it turned out the key was to invert the phase of the duplicated bass in the LFE channel--once I did that and re-encoded to 5.1, it sounded much closer to the stereo + LFE file I've been using for comparison. I'm presuming that somewhere in the upmix process, the phase of these bass effects became reversed, so that it was partially cancelling itself out. Now it combines the way it should. The entire principle of spreading a stereo source over more speakers is based on phasing tricks, adding and subtracting the channels together in various ways, so I suppose it shouldn't come as a surprise that this could happen.

So, now that it's taken care of, expect to see the final 5.1 version made available soon! It took a bit longer than I expected, but you can be assured it will all sound exactly as it should.