Here's a Sine Wave exported from FL, plays perfectly fine as did the other file. Upon importing it into Sonar on a Blank Project it changes the audio.
 
Sine Wave: https://instaud.io/417
Sonar Sine Wave: https://instaud.io/418

I am on my phone so can only read this. I did notice your FL export is 32 bit float, so not sure if this is an issue with the import. Does this also occur if you export a 24 bit file from FL?

mettelus
I am on my phone so can only read this. I did notice your FL export is 32 bit float, so not sure if this is an issue with the import. Does this also occur if you export a 24 bit file from FL?

Just tried and Sonar does the same thing to a 24 bit file.

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.
 

I just pulled the FL file into SONAR and also noticed that it is a groove clip. Without the exact tempo of this file,  "bouncing to clip(s)" will modify the file enough that I cannot phase test it in Audition.
 
I have never used FL, so not sure what the export dialog looks like; but either a generic wav file (or Broadcast wav) is preferred, especially when pulling into another program.
 
To Craig's point... I imported it into SONAR with a tempo of 120 (default), so the file was massively different than the original. (8.000 seconds versus the 11.048 second original (FL clip)).

You're right. I was tracking out my FL Studio files with the "Save Acidized" option checked, which saved the wav file with Sony Acid meta-data. Now I know not to have that option checked. I didn't even notice that all of the files I imported into Sonar were Groove Clips.
 
Thank you for figuring this out, I thought I was going crazy hearing things at first. Hopefully this helps anyone else that has this issue in the future.

BTW if you're into Acidized files, SONAR has really nice editing capabilities and construction capabitilities...one of its unique features. I think Acid is the only other program that lets you get creative with acidized files.

No not really, it wasn't even my intention to use the files as acidized files. I've just simply exported my wav files with the acid meta-data for a while now because the option has been checked by default and I never had any issues. But in the case that I decide to check it out I'll keep that in mind. It's cool knowing that Sonar reads the meta-data and automatically turns the files into a Groove Clip.