multi-harmony (SHMMR) method doesn't submit correct partitions for input data

The standard test alignment for SHMMR ( see http://www.ibi.vu.nl/programs/shmrwww/ ) should be analysed faithfully when submitted from the desktop application, but instead, it gives only 4 groups rather than 5 in the result (and excludes some sequences in the result too!).

Steps to reproduce:
1. submit example smad data to SHMMR - wait for completion
2. press the jalview button to open the applet and pass it to the desktop application with the File->View in full application menu entry.
3. submit the alignment and groups to the SHMMR service via the full application.
4. compare the result on the SHMMR web site, and note the missing 3 sequences which should have been included in the result.