EclEmma is a free Java code coverage tool for Eclipse, available under the Eclipse Public License.
ECobertura is a free Eclipse plugin for Cobertura, a Java code coverage reporting tool.
The eclemma plugin is nicer and more mature then ecobertura
Cobertura vs clover
No idea whether ecobertura has the same issue though;one factor may be that eclemma does not measure coverage correctly for exception handling code - it may tell you that code is not covered when in fact it is executed if you step through with the debugger the code is indeed executed
Why code coverage is different when measured by eCobertura and EclEmma?