I had the exact same observations about the remote action on my Freya+ during the whole day of using it after it came in two days ago. Next day it malfunctioned altogether, with remote not bringing the volume up all the way -- only the physical knob on the unit. Schiit said it was the motor, so today I sent it back and am waiting for a replacement.
I also felt upon the first day of listening that I might prefer the sound of my original Freya, and that feeling is again confirmed now that I swapped it back into the system. If I tried to qualify it any further, I'd say that the quality of the upper mids and highs was on the more crystaline side, almost too clean, almost thin perhaps. This is all of course subjective but I have a pretty decent trained hearing that I make a living with, and this system is incredibly resolving of all detail. The preamp goes balanced straight into Geithain RL901K; the room is tuned and quiet.
It could also be due to the difference in tubes -- the old Freya has a mix of Tung-Sols and NOS. Also lack of break-in time. I'll see with the replacement unit but for now I am definitely not selling the old Freya until I try the same tube combos in both of them back-to-back.