I suggest you should use a loopback latency utility app away from Sonar to test it. You then enter the offset into Sonar and test again with just Sonar, and then the waves should match perfectly.
 
I'm having a senior moment, I've forgotten what the utility is caused.

I remembered:
http://www.oblique-audio.com/free/rtlutility
 

Sorry that did not work... now I'm puzzled too.
You say you CAN'T tie the start of this behaviour
to an event(windows update, etc.)?
Can you provide an image of the wave?
 
Mel

Is it possible it's a clean redraw thingy - if having maybe 125% scaling on you system or something?
 
Haven't they updated some stuff to support scaling in Windows 8 and touch gestures etc?

Seems to be from the amp.
 
Test results:
 
(Already reported) Amp XLR Out + Mixer + Focusrite Line In = Wonky Wave
Amp XLR Out + Focusrite Multi In = Wonky Wave
Directly into Focusrite Multi In (Inst setting) = Normal Wave
 
This is quite strange because I have recorded this way before and didn't notice anything (on the CHC "Karyn's Got A Gun" I used this set up for the clean guits).
 
Thing is it sounds freaking AWESOME coming from the amp (the multi in DI sounds... well okay but it's DI which is why I'm using the amp). That wave is just freaking me out.
 
I guess at this point all I need to know is... how can this screw me up later on? It really does sound great so I am loathe to change anything.
 
Thanks for all the help guys. Gonna go back and read the recent posts.
 
This place is awesome.

Beepster
Seems to be from the amp.
 

http://forum.cakewalk.com/FindPost/3187066

Beepster
cleanish guitar output from the XLR line out from my old Traynor amp going into my Mackie CR1601 then being routed via the mixer's direct out for that channel into my Scarlett Focusrite 18i6 via one of the 1/4" line inputs on the back. In Sonar the input is set to a mono input (Right Focusrite Line 3 which is the mono input on the device).

After some thought I believe Dubdisciple is right.
Perhaps you have an unbalanced(1/4in.) output from the Mackie
you could try then compare the waveforms...
check to see if more than one buss from the Mackie is going to
your direct out;
 
more than one signal, summed to mono, WITH
dc offset could probably alter your input  to Scarlett
in the manner you describe(squashed tops).
 
Mel
 

Beepster 
 Seems to be from the amp.

 
Edit:I see that you are already on that trail... good job.
(Bloddy two-finger typing)

What Craig said Beeps. You have to allow for the fact that Sonar may be just fine and it's clearly reproducing a strange output waveform from the amp. If only the guitar amp shows this anomaly, it's probably in the amp, and probably a funky output tube. Try recording something else to eliminate everything but the amp as a cause.
 
If it's the amp I can send you some used but good tubes for free. It could also be a bad component but that's another story.

Anderton

Beepster
Seems to be from the amp.
 

http://forum.cakewalk.com/FindPost/3187066

Heheh... yup. I saw it but wanted to get the test results posted.
 
Thank you for the term "assymetrical distortion". It gives me something to research. Before I blather on I will ask this...
 
Is this going to cause me some unforeseen headaches down the road? If not I will ignore it because it sounds good.
 
Now to the blathering. This is not a "distorted" signal but the top part does indeed look like it is being run through a stomp box or something. The bottom half looks like the clean signal it is.
 
This is a solid state amp but a reeeeally old one (like late 60's/early 70's). It's a Traynor TS-140 if that means anything to you and it's a really nice amp. The XLR out is supposed to feed a board for live and studio applications but perhaps it's from before standards were really hammered out for that type of thing (IDK... I was even a spermulite until many moons after this thing was built). As I said I am running a clean signal but obviously the pre-amp is adding something (which I want) and there are two EQ sections (a 5 band graphic EQ and the usual T/M/B knobs). I have sweetened the sound a bit using those EQ's so maybe that's what's going on but I haven't really changed anything since the last project I used it. Maybe I should check those waves to see if it's the same deal.
 
Anyhoo... if this is normal and isn't going to be an arsehole down the road I won't get weird about it. Just took me off guard. It's really hitting the sim nicely. Sounds awesome for bass too (which I tried the other day for the first time).
 
Cheers.

ampfixer
What Craig said Beeps. You have to allow for the fact that Sonar may be just fine and it's clearly reproducing a strange output waveform from the amp. If only the guitar amp shows this anomaly, it's probably in the amp, and probably a funky output tube. Try recording something else to eliminate everything but the amp as a cause.
 
If it's the amp I can send you some used but good tubes for free. It could also be a bad component but that's another story.

Very generous, my friend and thank you. It's a solid state (TS-140 which you are likely familiar with) so no tubes needed. Glad you popped in. If anyone knows what might be going on with this amp it's you. Heck... you may have even worked on the darned thing at some point in its life. lol