Hi there, I'm not sure if this is a useful soluion to your issue, or if you've already resolved it...but in any case, I was facing a similar obstacle.
I filed online (not through the desktop version), so I can't say for sure if this will work for you.
In my case, the [Tax Home] page on the website was showing that I had started a WA state return. But while reviewing the state return tab, I'm told WA doesn't need to do this, so naturally you'd expect that'd be that. In my case, I ended up clicking on the state tab again selecting WA and [State Review] - from there I deleted WA state as a state return and then went tot he tab above [Your State Returns] I selected skip state return since. Going back to [State Review] I then selected Do Not Prepare State Return. and then selected [File] and was taken through to the home page.
As a note, I had already file my Federal return but it was still pending. The [Tax Home] page still displayed the State Return, but this time it said "Not Started" instead of in process. I clicked again and clicked the tab [Your State Return] to which I think selected skip and then again chose Do Not Prepare State Return in the [State Review] tab. I selected [Tax Home] and the state return was no longer present. Shortly after, m federal return was accepted. I'm not sure if it was just the timing with the federal return being in process and then being accepted that made the change occur.
I know this might not help, but hopefully there's something in there that can help you manuever around it. Even more hopeful you were able to file successfuly and the problem is't an issue anymore.
