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I20081007-0800. The new option about strictly matching JRE is not updated when the preference is changed via UI. We clean and build the project but that has no influence as a resource delta on a JRE container is currently needed to trigger this. The easiest solution is probably to register a builder that clears the marker on clean and creates it on full build.
Fixed by refactoring EE error reporting into an compilation participant. Whenever a project is cleaned/built EE errors are potentially created. This appears to work well for all situations - modifying a build path from the UI, by editing the .classpath file, and by changing problem severities.
Please verify, Curtis.
Verified.