Thanks - lit's a bug. I get the same problem.
For me, the Flash CS5 compiler is executed, but there is a problem with the Amethyst message saying that everything is OK. The way to get round this is either
1) copy the line from the output window (for my test project)
"C:\Program Files (x86)\Adobe\Adobe Flash CS5\Flash.exe" "C:\Users\dermot\AppData\Local\SapphireSteel Software\Amethyst_2_10.0\Temp\uzncmizi\imageViewer.jsfl"
and paste it into a command prompt window. This will run Flash CS5 with the commands specified in the .jsfl file and you can see what's going on.
2) ignore it - the Flash CS5 compiler has actually run and built the SWF. If there were no syntax problems, everything should be OK.
When you try to debug, the build system will not rebuild if the SWF file has been created by the Flash compiler, and you should be able to debug it.
We'll release a fix in the next few days and I'll post a message here with the links to the fixed version.