Do the two sources sound the same?
If you’re using any kind of distortion effect, the output of those will vary a lot depending on the level of the input signal, so if one source has a lower level than the other, that could explain it. You’d have to match levels before sending through the effects chain. If more than levels vary (different mic positioning, different room) then you have to match the complete tone before the same effects chain will yield the same result.
If the two sources have identical character and level to begin with, you have more of a mystery on your hands. What happens if you merge both clips into one and effect that clip? If the difference is still there, it’s down to the sources being different, if the difference disappears, it hints at a difference in the effects chains. That should help to at least pinpoint the issue.
IHTH,
JC Boulay
Technical Director
Audio Z
Montreal, Canada
http://www.audioz.com