And already a SAM related problem...

[invictus005]

The OP is not actually using the wrong SAM profile. In his first post he says ' I'm using Bowers & Wilkins speakers with correct SAM profile'. Later he is trying other B&W profiles for testing.
I think SAM may be reacting to subsonic content i.e. tonearm/cartridge resonances. SAM should have enough deep bass filtering to avoid this so something is not right. Try enabling the high pass/subsonic filter of the amp. This ought to fix the problem while you research the cause and get it resolved properly

Thumping noise is on both analog and digital sources, just more audible on vinyl. If I set up high pass rumble filter on the output, 15Hz at 24dB, noise goes away, but then it doesn't sound as good. Noise goes away with RIAA 1976 (as it has a forced rumble filter), but is present on RIAA 1953.

I've now tried additional firmware versions and everything with SAM1 works fine, with SAM2 it has the thumping problem.

One thing to clarify, my LE 120 did not come with a remote, so I'm using iOS phone app for controlling the functions, therefore SAM is always either off or on 100%. I cannot adjust SAM's % level.

I've ordered a remote and once it comes in, I'll be able to test SAM2's % levels below 100%. I've been reading this forum and it seems that many people have had a problem with SAM2 and rumbling noises and most run bellow 100%.

But this is still upsetting.