I can't help you with well experienced advice, but what I've noticed with tube amps is that they produce(or make you imagine) more bass around 70-100hz. Could it be possible that higher bass is masking your lowest notes?

Since I'm still ampless, I had to play with my tube pre. The only thing I could do was to connect it with a CD player and my sub.
What I can honestly say this that my REL played much tighter thru BAT than my tube integrated. But I need to tell you that my REL is hooked up thru speakers binding posts from my tube integrated, while it was hooked up thru SE outputs from my pre. Also, my sub doesnt go below 30ish so not sure if this can help you in anyways, but I'm curious if you have also noticed about higher bass frequecy. If so, do you think that could be the reason?

JRA