You get much better results if all sequences are full sequences. Maybe you should delete all short sequences from the dataset, and create a new pt_server index file.
The pt_server index file and the currently loaded database should be nearly identical.
The program never stops. If you think you cannot wait any longer press kill and inspect the results.
The target group and nothing else should be marked. Be sure that you don't forget species to mark, especially if you are not working with the complete tree.
The buttons at the bottom of the window:
'Compute' calculates possible results
'Open result window' : This button can be chosen to go directly to the result window without calculation(i.e. to load an old result list)
The colors for the probes can be specified in the ARB Properties->Tree:
Color and Fonts