Mysterious Flange Solved
One of the basics of sound on sound is that when two identical pieces of music are played at exact the same time, but with one of them delayed ever so slightly, you get the famous flanging effect (a type of phasing effect).  At the waveform level, flanging comes from the sweeping comb filter effect caused by that tiny delay between the two pieces, but it’s not supposed to happen if the two sounds line up exactly.
And yet, a few moments ago, I ran into a mysterious flanging in Logic Pro (in which I make my tunes) when overlaying the two yellow tracks above.  As you can see, the two match up exactly within the cycle region (that green bar up top), so there shouldn’t have been any phasing whatsoever (I confirmed their alignment by zooming in as far as Logic would let me).  
To troubleshoot, I first turned off the Platinum Verb insert in my Vox Aux bus, as well as the Fuzz-Wah I was using.  Still flanging.  
Next, I muted the Aux Send altogether.  Still flanging, so it wasn’t the Aux at all.  
I even tried muting the Stereo Delay on both tracks; not that it should have mattered, since it’s not a Flanger unit, but this, too, yielded no change.  Failing all of this, I solo’ed just the two tracks and kept starting & stopping the cycle loop—and I finally found a clue: sometimes the flanging happened; sometimes it didn’t.  That’s when I isolated the culprit.  
In Logic, when a cycle starts, if there is active audio right before the cycle region, a little bit of that audio is activated during playback.  In my case, a millisecond of audio from the leftmost audio region was spilling (Stereo Delay and all) into the actual cycle region—and that one millisecond of extra audio is all it took to cause flanging, perhaps abetted by the Stereo Delay effect.  After I muted the yellow piece in red, the flanging went away.  Yay!
So, the moral of the story?  Watch out for adjacent audio regions, even they’re outside the cycle region, and beware of flanging if you have two identical audio regions playing simultaneously!

Mysterious Flange Solved

One of the basics of sound on sound is that when two identical pieces of music are played at exact the same time, but with one of them delayed ever so slightly, you get the famous flanging effect (a type of phasing effect).  At the waveform level, flanging comes from the sweeping comb filter effect caused by that tiny delay between the two pieces, but it’s not supposed to happen if the two sounds line up exactly.

And yet, a few moments ago, I ran into a mysterious flanging in Logic Pro (in which I make my tunes) when overlaying the two yellow tracks above.  As you can see, the two match up exactly within the cycle region (that green bar up top), so there shouldn’t have been any phasing whatsoever (I confirmed their alignment by zooming in as far as Logic would let me).  

To troubleshoot, I first turned off the Platinum Verb insert in my Vox Aux bus, as well as the Fuzz-Wah I was using.  Still flanging.  

Next, I muted the Aux Send altogether.  Still flanging, so it wasn’t the Aux at all.  

I even tried muting the Stereo Delay on both tracks; not that it should have mattered, since it’s not a Flanger unit, but this, too, yielded no change.  Failing all of this, I solo’ed just the two tracks and kept starting & stopping the cycle loop—and I finally found a clue: sometimes the flanging happened; sometimes it didn’t.  That’s when I isolated the culprit.  

In Logic, when a cycle starts, if there is active audio right before the cycle region, a little bit of that audio is activated during playback.  In my case, a millisecond of audio from the leftmost audio region was spilling (Stereo Delay and all) into the actual cycle region—and that one millisecond of extra audio is all it took to cause flanging, perhaps abetted by the Stereo Delay effect.  After I muted the yellow piece in red, the flanging went away.  Yay!

So, the moral of the story?  Watch out for adjacent audio regions, even they’re outside the cycle region, and beware of flanging if you have two identical audio regions playing simultaneously!