web service panel only displayed when job is finished, not during progress

I've noticed that Jalview sometimes does not report progress during the task execution instead it displays all the execution log at once at the end of the task. It is not clear what causes the issue.
I'd recommend you double checking how the progress is reported. Also to reduce the possibility of an issue from the JABAWS side, I'd suggest to include at least 5 seconds delay between task submission and the first pull operation, to let the statistics output file to be created in the fist place.

Thanks,
Peter