I just got Bias FX after using the LePou Legion amp sim for a few years. Every stock patch sounds muffled/like it's coming from behind a wall, and I only got one of my custom tones to sound reasonably clear and present after cranking up most of the treble settings.

All the demos I've heard on YouTube sound great, but even if I download their exact setup from the tone cloud it still sounds very muffled compared to what I hear from the videos. It's a clear difference so I don't think it's a matter of being in a full mix or not.

I remember having the same problem with the free sims and the Legion was one of the only ones that didn't sound like it was covered by a blanket.

Could this be caused by a problem with my pickups (EMG 81-7 and 707) or my interface (Scarlett 2i4)?
I have those pickups in my 728, and a similar focusrite unit and sims work ok for me. BIAS can feel pretty muddy without some extreme treble boosts, but I think that's part of the realism. Be sure you are really doing an apples to apples comparison, make sure they aren't using separate impulses or something
Whole bunch of things here to consider. You gotta start at the beginning of the chain and work your way to the end:
Guitar (new strings, tone and volume knobs up, pickup wiring correct, fresh 9v battery, and guitar jack is in good condition)
Cable (try a few different ones)
Interface (if you have a low cut switch, try it; make sure youre getting enough gain for your signal; check your DIRECT monitoring on your interface totally dry and compare that sound with the RECORD monitoring sound totally dry- if they sound the same, then the problem is before your interface. If only the record monitor signal sounds bad dry, then there is something going on on the software end)
Quote by suckmahnuts
Watterboy, I love you.

Quote by davrossss
You are now my favourite person on UG.....You write cool shit.

Quote by wannabestoner69