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[ JDK VERSION : 1.7.0_55 ] From time to time I have troubles with error badges. E.g., if there is an error badge on a file, but there is no red marker visible in the editor to determine it's location. In such a case I have to invoke Compile to find it, which is not possible with disabled Compile action.
Unfortunately it's not easy. When Compile On Save is enabled it copies the classes from caches into the build/classes before actual run. So the compiled file will be overwritten by CoS if it was modified from last run. As far as I remember there was long discussion when CoS was introduces which actions should be enabled and the conclusion was that only "Clean & Build" is save as it deletes everything and compiles everything. The enabling has to be done in action provider (java/project) but I don't believe it's save to do it.
Added Honza L. to cc as hw knows most about CoS project actions integration.