Here is a better of of explaining it....
"So for some of my pad/organ melodies when I input them into Newtone which is basically just this plugin in fl studio that analyzes the pitch patterns. It gives an incorrect reading (or maybe it's giving a correct reading who knows at this point as I have been spending all day trying to figure it out) Anyway the melody that I inputted into the piano roll is D#-G#-D# however when I input it into newtone it says the melody is actually G-C-G. This happens with almost all my pads/organs. If I use a sharper sound like a piano there is no difference in the reading. Even if I enter in a bass melody there is no difference. Do you think the issue is just the pad/organ presets themselves? Are they already out of key to the point when I input them onto the piano roll as D# it is actually at G? Is that even possible?"