This definitely seems to be a bug. It looks as though custom properties cannot be used when you are including modules.
What were you trying to do with the custom property? There is probably a simple work around by defining a global text attribute with the value you wanted to put in the custom property.
In the meantime, I will raise this as a bug
So just to be clear, they DO work perfectly for everything other than the project level. I noticed that you cannot define Entity or relationship level if the module defines them, so that is no big deal, and the attributes work so that cool.
Anyway, thanks for letting me know that I am not crazy
The solution you gave is actually what I did at first, but I found another way to accomplish what I needed. Definitely log the issue though as project level properties can be a powerful integration tool!