I've made changes to the scripting engine to address these issues and now the sample script above works as intended.
Here's a direct link to the updated flashfxp.exe
http://www.flashfxp.com/testr/5/ffxp5.0.0.3805-r2.zip
I have tested all of the scripts I have and they all seem to work as expected with these changes, please let me know if you encounter any situations or problems with existing scripts. I have to wonder if there's any existing scripts that were designed based on the flawed ordering. I sure hope not.
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