I know this post is over a month old, but I'm having the same trouble with the PSD export. All of my folders are flattened into separate pixel layers, however it was from a fairly complex imported PSD that I was exporting.
So I've been using the trial (and have now purchased the software) and raving about your software to all my coworkers and friends and while it's awesome, the consensus has been that "we have no use for it if it doesn't integrate with Adobe's software both ways." I think the use case for a refined .psd or .ai export feature is that you've broken in an Adobe dominated market. If a freelancer/contract designer does, for example, a web design for a company, chances are that company will require them to provide a PSD.
All that being said, I think your software is far superior to both Photoshop and Illustrator (from what I've seen so far) and you already have my money :). I just wanted to chime in on this because I would be very interested to see how the export feature develops over time. I know that it is no small task to implement this, especially since Adobe most likely won't like the competition... but I think it's very important nonetheless.
Keep up the good work!