I'm now able to make Protobuf work. All I had to do was to configure my mecab dictionary to use utf8 and then reinstall it. After which, protobuf works find :-)
However, when running the StandardTaggerTest and the LocalProtobufTaggerTest, both executed at roughly around 3000ms for 1000 executions. I did not see any speed gains. Is this expected?
On a side note: compared to GoSen, CMeCab-Java's StandardMeCabAnalyzer seem to be slower for indexing (haven' tried searching though). In my current system, with GoSen indexing takes about 40seconds, while swapping that wtih StandardMeCabAnalyzer, it jumps up to 80secs. Is this expected as well?