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FB 4.5. I know the old FB has a file .markers you could delete, but where does 4.5 keep these?
Sometimes the markers will disappear with "clean", but not always.
Do you sometimes see two copies of all your errors? If so, I think you might have a project that's created in a different location than your source code http://flexdiary.blogspot.com/2012/07/when-good-flash-builderflash-pro .html
No doubled errors. And my source code (src) is below the project folder. The errors are "orphans"- that is, they were valid errors once, but after correcting and rebuilding, they do not go away. Sometimes a "clean" will remove some of the them.