One of the commonest causes of 'strange behaviour' that our users have reported seems to be Jalview running out of memory. Memory errors can cause some operations to fail silently - with no warning, annotations may disappear from the alignment window, and web service calculations (apparently) never finish.
Jalview now exports images and graphics using the same settings as the alignment display window. Just set the font and font size, and the layout style (normal or wrapped) using the View menu.
If you do want to specify portrait or landscape, you could use the File→Print dialog box, and redirect the output to a file.
Yes. The Jalview Desktop has a number of command line options, but how you access them depends on the way you want to launch Jalview:
1. If you use Java Web Start to launch Jalview, then on some versions of Java Webstart you can start up Jalview with a specific file by typing:
javaws http://www.jalview.org/webstart/jalview.jnlp -open yourFileName
You need a computer that can run at least Java 1.7 to use the full Jalview application (unfortunately this excludes users with older Macs - sorry). If java is installed, then the 'Launch Jalview Desktop' link at the top should work (if your browser asks you to save the application-x-jnlp file or choose an application to run it with, look for 'Java Web Start', or locate your java installation directory and look for the javaws binary).