Ok. It took me a while to think about this a little more, but I'm still not getting it. How do I determine where the phase cycles begin / end? I'm not sure where I could find that out.
Sorry. I can't really phrase a good question. I'm still confused on how to fix this. I may just have to split the stereo. Is that a common practice among the veteran sample-makers?
Also as a little background about this sample here:
I made this sound by using a VST (Crisalys to be exact here's a picture of the program config)

However, I found that I wanted more granular control without using PCs all over the place (plus I can't figure out how to make vibrata work in the VST). So I went into a playground file, played a note (e.g. C4), and used a main volume PCs to then turn it off and then turn it back on. Then I repeated the process, playing a note halfway up the chromatic scale (e.g. F#4 ). I then continued that for 3 more octaves, and then exported that "song" to a .wav file. Then I reloaded the whole thing as a sample, which attached to an instrument, and proceeded to split the sample into smaller ones, using the PCs silences to denote when one note stopped and began, and trimmed a little of each sample off each side along with the silences. What you are looking at is a snippet of one of the notes I used in the final instrument.
Now, for a little more clarification: (WARNING: BIG PIC DUMP...sorry)
This is a full arbitrary sample, already resampled for loop smoothing:

This is a close-up of the loop beginning:

And finally, the loop end:

In most cases, the end didn't really resemble the beginning (this may have happened here because of the smoothing), but even with the smoothing I'll still be able to detect the loop wrap-around point.