We're very conscious of the possible troubles with the designer-developer relationship at LayerVault. Hell, the entire product is almost built around addressing exactly that point.
There's still a long way to go before we see that next big leap in improvement. Quick iteration is key.
Coming from an architecture background I always find odd that the coordination and managing roles in the software world are usually reserved to engineers.
I think it's temporary. Maybe a by-product of the fast pace with which technology evolves, which puts an emphasis on engineering, and definitely a very long lack of interest from traditional designers in software projects.
This is now starting to change.
I struggle with this as the lone designer on a small team of engineers/programers for a startup. I finally sent out a company-wide email explaining how everyone single one of us was a designer - I focused on the visual design and the user experience, but every line of code they wrote affected the user as well. Bloat and bad practice leads to a sluggish website, which can be frustrating to the user; buggy elements or pushing to product before an element is ready for prime time weakens the impact of the product overall; etc. It was really well received.