I think the reason is simpler - there is little evolutionary pressure. Coming from an ISV background, you will see that better designed user interfaces almost always sell better. Complicated or difficult to understand user interfaces will sell worse. So there is some type of pressure in commercial software to go for somewhat better user interfaces.
This pressure does not exist for open source software in the most case. If the people who are involved in the project find that it solves their needs, they don't see any need to modify it to fit the needs of new users. So the interface stagnates at what the core contributors are familiar with.
This pressure does not exist for open source software in the most case. If the people who are involved in the project find that it solves their needs, they don't see any need to modify it to fit the needs of new users. So the interface stagnates at what the core contributors are familiar with.