This is one of the more irritating limitations in FileMaker.
If your table of values is fairly small and you only need one field in your value list (You aren't using the field 2 option for something else), there is a trick that can display the list values in a customized order by putting a unique number of space characters in a field in your source table and using it as the second field with the sort values by 2nd field option enabled.
This is such a problem in one of my DB's that I finally set up a global text field where a script places a list of all values from the table in an order controlled by a number field where the user sets the order. The user then uses the edit option so as to be able to manually copy and paste the contents of this text field into a custom values field each time he wants to change the value list order. That's a really awful Kludge, but it was the best I could come up with at the time.