I bought my 306 used and it had ~300 hours on it when I got it. I really didn't hear much in the way of break-in when I put it into my system (about 9 months ago). It continues to sound great on RBCD/HDCD and SACD.
As to the filters, I almost always listem without upsampling. In that mode the signal goes through the PM200 HDCD filter which is a high quality filter. RBCD sounds really fine in that mode. I've experimented with various amount of upsampling but I don't find any of them sounding better than the 44.1 setting. Strangely, when I use 192 the sound is louder by about 1 or 2 dB. At first it seemed to sound better but I have chalked that up to it being slightly louder. Anyone else experience this?