Hi,
JaCoCo works on debug information in Java class files. Eclipse has its own compiler which creates more detailed debug information in certain situations (e.g. multi-line expressions). But this should cause only a minor difference (and should not have an impact on line coverage).
Also note that we added a few filters to JaCoCo (for unwanted compiler artifacts). Depending on your Eclipse version you might use a older JaCoCo version in Eclipse.
For a detailed discussion please provide
1) An example snippet with its coverage values in both reports (Screenshots)
2) The version of the Maven plug-in.
3) The version of the EclEmma plug-in.
Regards,
marc