automatic calculations not enabled when alignment imported via command line argument

Using the 'Open in desktop application' option from the applet should open the alignment data shown in the applet in the desktop application complete with any automatic annotation rows. However, none are added.

Example URLs:
http://www.jalview.org/services/launchApp?open=http://www.jalview.org/examples/RF00031_folded.stk&colour=Purine/Pyrimidine