Ok, to clarify: All Abilities must be moved around at least once. Failure to do this will result in Abilities being out of place in the Token Action bar. Example: You set up your Abilities, move them into the desired order, and then you create a new Ability. This will have the possible effect of messing up the Token Action order. Also, are you using Macros (settings tab macros) on the Token Action bar? That will also mess up the order. If you have moved all Abilities and you are not using Macros in your Token Action bar then please send me a join link and I will take a look.