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.