If you created the layers with an application token then the layers are associated with the application, not with your account. We're working on a fix to make the account/layers page show layers that were created by applications you own as well.
We have updated the layer list on the developer site to also show any layers created by your applications! You can also now create layers for your apps from the site, and use our visual trigger editor for those layers as well!
Aaron, the visual trigger editor is a great help. I'm not sure why place/list returns an empty list, while I can delete and create accounts with the application access token and view them on the visual trigger editor?