My Sonus Faber Amatis have weak bass even though I'm running ML 536s--800 w/ch into 4 ohms

BTW, if your room is reasonably rectangular, I suggest examining the results from the AM Acoustic room mode simulator here.

I don’t know where you acquired your speakers, but if you bought $30K Speakers from a Dealer and they didn’t care enough to set them up for you, then you purchased from the wrong dealer! The specs of your speakers says the go down to 28Hz which is below what most music goes down to so your speakers are producing the desired frequencies, but their position in your room is creating a suckout at your listening position. Your Dealer should have assisted with placement so this doesn’t happen or suggested ways that you can mitigate the problem. In the end for some speakers and positions the only solution is Subs which can be placed randomly to achieve the best position. 

I would recommend getting your room measured to see where you stand graphically.  This will show any room suck outs where there is a bass void.  Room EQ Wizard is free, you just need an appropriate mic.  Maybe you have a friend nearby who could do some measurements?

Obviously there is something going on. 

It does sound like phase thing, this is easy to test.

Play some bass, move the balance full left, listen, then full right, does the bass go up at each extreme L/R? If so, it's a phase issue. 

Next thing would be is everything hooked up properly? Would suggest pulling everything apart, cleaning all contacts, hook it all back tougher. 

Of course speaker placement, this will make the biggest difference. Sadly best bass is usually not the best tremble on placement. You may be sitting in a null point, will just never get good bass. Again, play some bass, walk around the room. Does the bass go up and down? If you move from your listing spot is there more bass? If so, null, you got to move out of it. 

You said you have a wall of glass? Need to treat the windows, glass walls are about the worst you can have in audio.