Help me like my ultra

I highly doubt it's cables. I've never heard a guitar cable change the sound so much that turning a few basic controls didn't account for it. It sounds to me like it's the power amp and/or Global EQ. If you crank your presense, treble, damp, have the bright switch on and it still sounds like a blanket is over the amp, there's something wrong. I would bet it's most likely not the axe fx hardware since the sound is processed digitally. It's not like a tube is bad or something. If it was an Axe FX hardware issue, it wouldn't roll off the highs... it would just stop working.

Like mentioned earlier, strip the chain down to simple components. Make sure the Global EQ is flat by pressing the "Global" button and checking the Out1 and Out2 pages. Create a patch with nothing in it but an amp block and shunts. Take out the BBE. Just go Axe - Power Amp - Cab. If that sounds like crap, try a different power amp, then a different cab. Don't assume anything.
 
Aside from what's been mentioned, the first thing I'd suspect is a major impedance mismatch between one or more of the devices in the chain. That can easily kill the top end and blanket the tone. I'd start by just plugging a stock-spec guitar into the front of the box and connecting the line outs directly to a board and studio monitors or other full range audio listening environment (as opposed to a guitar amp). If it still sounds dull then, and all the internal settings are normal (like with a not-too over the top factory preset), then there may actually be a hardware problem. If not, then I'd go through each piece in your chain and see which one (or more) is the problem.

I had a pro player in my studio a while back with a very complex rig and an EMG-equipped custom guitar who wanted to try out my vintage Tele through his effects. It sounded horrible - just like the OP described here (no high end, blanketed, dead, which is of course NOT what one normally gets from a Tele), and I was very concerned that the pickups had somehow crapped out (it hadn't been played in a while). When I checked it later, straight into my vintage blackface Princeton Reverb, all was well - it screamed treble just like it should. The problem was clearly an impedance mismatch between the stock instrument and my friend's custom FX rig.

Much to my relief... : )

I think this could quite likely be what's causing your problem too.
 
The first thing I would do:

1. Hook up your Axe FX for direct recording into your sound card.
2. Find a thread in the "Share Your Presets" section of this forum that has a recording with a tone you like and also has a link to download the sysx file
3. Download the sysx file and load it into your axe
4. Audition the patch

By eliminating everything but the Axe FX and your guitar and then using someone else's exact settings, you'll be able to compare exactly what comes out of your axe to exactly what comes out of someone elses. to me, this is the best way to make sure you're comparing apples to apples. Otherwise there are too many things that could be causing the issue. The first thing you've got to do is test the axe 100% by itself. Once that sounds good, try creating some patches and playing with the different parameters. Once you've got the hang of how to elicit the different sounds and results you want, you can focus on getting your axe to play with your other gear. Because then if you find that there's some funky dynamic between your axe and another piece of gear in your chain, you'll be able to identify exactly which piece is causing it, and you'll know the axe fx well enough to know how to compensate for the funkiness through the axe fx's controls.
 
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