Having read a post of Tom Hopkins where he told a windows user to turn off hyper-threading, I used CHUD and disabled one of my processors. I loaded the .gpo file I have had trouble with and sure enough, in the Kontakt player, crackle is almost gone, only sometimes at the start and finish of a note.
Could the GPO file be corrupted an any way? if I open GPO Studio and load one instrument, it works fine. Also If I opened my saved .gpo file and deleted the instruments in 1 of the 3 players, the remaining two would play without crackle. If I opened another play and added instruments, everything played fine.
Back in finale, with a 4 or 5 channel piece the crackling/popping was almost nonexistent with one processor. Even with the troublesome .gpo file it was minimal. I could pause in the middle of a song, add the second processor back on and the popping started immediately, at least once per measure. In the single processor mode, finale was alloted from 8 to 12%. (I guess this shows how wrong I was in my other post.)
Ambience is bypassed during this time.
I hope this helps whomever is trying to fix this issue.
Seems sad to have machine that you have to disable one processor because of a program that will not work well with both of them working. But to put things in perspective, at least I can use the program with both processors, unlike Apple's own APack, which will not even run with both processors going.