[Solved] Amp sim odd clipping issue - Pickup gain issue

Just to be clear before I take off with this... I do not run amp sims often, so my setup may be what is FUBAR in this scenario...
 
I just upgraded to TH2 and ran across an odd clipping issue and wanted to throw this out to see if someone had insight as to what is going on. In short (will describe the setup detail below), I have been running TH2 stand-alone thus far, just to check it out, and after setting up, using the "IN LEV" to adjust level based on a full G chord then play (cycling presets). Then, I suddenly will get nasty clipping on the low E (and sometimes A) strings solo. (The chord with IN LEV is about -6dB).
 
For setup, I am running a guitar->Saffire 24 PRO (Inst channel)->TH2 (just running presets in stand-alone mode)
 
The guitar - I have a custom built guitar that I put DiMarzio D Activator pickups in last year simply for the highest/cleanest output without the need for batteries (I hate batteries).
 
The Saffire - I have been using Inst In and resorted to putting its compressor in play just as a limiter and could still get the clipping at times.
 
TH2 - nothing more than using IN LEV and running through presets.
 
Initially, I was thinking maybe I had inadvertently attacked the low E enough to make it buzz the frets, and the pickups were having a hay day with this, but when it does trigger I will then stay on that string and attack it lighter and lighter, but still get it to clip (staying low on the fretboard, so I am still scratching my head with this). I am not sure if I should be using other settings on the Saffire (the line in has much lower gain, so maybe the Saffire is contributing to this as well).
 
Anyway, after having this happen enough, I end up lowering and lowering input levels and seem to still trigger this (somehow). Oddly enough, since I can do a side-by-side comparison, I switch over to GR5, do not see the same issue, and played that for 3 hours instead.
 
I have a few variables in the mix here, but clipping one string is making me think "fret buzz" but it cannot detect this. Lower notes have more power, so is possible that an attack on a single string is more amplitude than a chord, and the Saffire settings may not be ideal here (the Inst In and D Activator pickups may be a bad combo). Then shifting to GR5 and not having the issue just blew things out of the water on me, so I gave up.
 
Any advice on what I might be doing wrong, or should be doing right would be most appreciated
 
 
 

Thanks for the reply. I am leaning a lot toward the Saffire being my true issue. I had used an old GNX3000 a couple months ago as an ad hoc "DI box" and ran that into the Saffire as a line in without any issue at all. I am thinking that the difference in the setup came from using the "inst in" on the Saffire (I am not sure what that is doing to boost the signal), but am suspecting it is the real culprit. When I get a chance later today I will check this out in more detail.
 
Maybe I was just getting lazy about running cables around (I fell like I am in a ball of spaghetti when I do that).

I am actually glad that this happened, or I might not have delved as deeply into this as I did...
 
First, I started with the Saffire, put it back on line in, and stripped of all comp/EQ effects... my reasoning was 1) eliminate the extra spaghetti from another piece of hardware 2) set a quick standardization test, and 3) I assumed the "Inst in" was inserting a gain that I did not want to deal with (and exacerbating the true issue)
 
Second, I took two other guitars with stock pickups and checked gains on the low E versus the high E on both the neck and bridge pickups. For both guitars the low E was a little hotter, but not significant (around 3dB).
 
Third I used the guitar with the D Activator pickups and the low E was over 12 dB hotter than the high E! Running that through any kind of gaining would just magnify and clip (as I was seeing).
 
So the "solution" was merely to back off the pickup on the low end, but by far more than I ever would have anticipated... they had to be backed off 3/16" to level the signal across the strings which I have never seen before. I brought them back up a small amount to ~3dB hotter (only a couple of turns), and everything was resolved.

LOL, yup  
 
Edit: I re-titled the thread after my last post and sort of killed the punch-line, but never in my life have seen pickup requiring that much tilt. (Unfortunately) my amp set up is not bass-heavy, and was masking the issue a great deal, so I am actually glad this happened.
 
Ironically, when I re-built this guitar I meticulously wired it with 6 switches to get all possible serial/parallel configurations out of it, yet they were not as dynamic as I was shooting for... turns out that the extreme gain in those low strings was the problem there as well. All of the tone variations fell into place "as expected" after the gains were leveled out.