Don't know if this topic can interest large part of Stencyl user, but I'm sure can interest a little part of developers.
To debug your Stencyl project you must debug the generated project you can find here: %APPDATA%\Stencyl\stencylworks\games-generated
After game selection you must create a new Flash Develop Project with the following data:
0. Go to %APPDATA%\Stencyl\stencylworks\games-generated\NameOfProjectYouWantDebug and then copy project.xml in other folder.
1. OpenFL Project
2. Location: %APPDATA%\Stencyl\stencylworks\games-generated\NameOfProjectYouWantDebug
3. Choose a project name
4. Leave 'Package' blank and 'Create Directory' unselected and create
5. Copy saved project.xml in %APPDATA%\Stencyl\stencylworks\games-generated\NameOfProjectYouWantDebug
6. Start Debug
7. Start Release
If Release is ok and Debug give you some problems, remember: Flash Develop need to run with jre 1.6 32-bit (you can find all you need in Flash Develop FAQ).
David.