Why do some custom properties go under variables and other go under custom properties? I want all my custom properties to be listed together, there is nothing different with the property that I can see that would place it under a variable? 
from my experience with this, is you have to assign them to a group or they just end up in the Custom properties group, otherwise they act differently.
Currently, a custom property with no group appears under Variables when it applies to items (on an item or on a takeoff with an inline item). Otherwise, it appears under the Custom Properties group.
We're open to feedback on whether all upgrouped properties should show up under Custom Properties, or if we should keep the current behavior for items.