[Solved] Audible Difference On Imported Audio

I think I found the issue. When I bring the FL Pad into SONAR, it's converted into a groove clip (loop). That means SONAR thinks it's either a REX file or Acidized file. I don't know what format FL Studio uses. When I bring in your exported SONAR file, it's not looped and apparently has no looping metadata. With a loop containing metadata, if SONAR's tempo isn't exactly the same as the FL project, then you'll hear the kind of artifacts you describe.
 
To diagnose further, import the FL Pad into SONAR. Then click on the clip after you import it and type Ctrl+L to unloop it; I'm pretty sure the artifacts will go away.
 
Note that when you export a loop from SONAR, it will always export as a WAV file, without any looping metadata. To export a loop from SONAR, open it in the Loop Construction window that adds the metadata, then choose Clip > Save Loop from the Loop Construction window.
 
In any event, this problem has nothing to do with the accuracy of SONAR's import/export function given that I could null the original file with the exported/imported version. However, I unlooped the FL file first so it was a normal WAV file prior to exporting and re-importing. You need to look at how looping functions are handled in FL export, how they are handled once SONAR receives the file, and if there's anything you need to do in SONAR to accommodate the file.
 
My best guess pending further data is you exported the loop at one tempo, but imported into SONAR set to a slightly different tempo.