This is an issue we're aware of and plan to correct. The issue is the custom fields don't remain in the order you arranged them in when you assigned them to a category. They remain in the correct order when creating the entry, but return to alphabetic order once the entry is created and printed. You will notice when you go to the "Custom Fields" section on the manage page that the list of fields appear in alphabetic order. This is the default order.
You can override the order by assigning a sort value to the individual fields. Open up the fields and you see an option for "Sort". You can sort them 1,2,3, so on; or 1, 1.1, 1.2 and so on.