Autokern should only be run once. If you need to edit the kerning pair adjustment lookup or the kerning classes, use the OpenType designer. You can clean up unused lookups and features in the OpenType designer, or clear the script entirely and start over if kerning is all that you have added.
The problem with a fully automated process is that it lacks any knowledge of text. It just looks at the shape of glyphs in creating the classes, then pairs each class with every other class, calculating the optimal spacing based on the glyph spacing factor input by the user.
Take a greatly simplified example of kerning A, Á, À, Ä, Ã, Ā, L, T, V, and W. FontCreator will probably create one kerning class for A, Á, À, Ä, Ã, and Ā, another for L, and one for T, and one more for V and W. It will then generate kerning pairs for each class with each other class. Four kerning classes and ten glyphs produces sixteen kerning adjustment pairs: AA, AL, AT, AV, LA, LL, LT, LV, TA, TL, TT, TV, VA, VL, VT, and VV. Multiple that by 6 in the A Class, and 2 in the VW class, and we have 192 kerning pairs already.
Doing it manually, I might create the same classes, but I will only kern those that I know will need it: AT, AV, LT, LV, TA, and VA. That is only six pairs x 6 x 2 = 72 kerning pairs.
Now, think what will happen, not with ten glyphs, but 2,000 glyphs! You will get a whole bunch of pairs that are not wanted, and have to be deleted.