This post is almost 6 years old. Still, this has not been fixed. I've worked with many software developers. This is not a difficult fix. Certainly not something that should take this long.

This issue is the reason we are demoing Xero. We are a not for profit, so we use Class to track functional expenses to produce our Statement of Activity by Functional Expense as required by FASB. This also makes completing our annual Form 990 much easier. 

We intended to use Location to track the different departments for budget purposes. And key expenses such as legal fees are often on one AP invoice yet split among departments.