OK, I have an idea. Is it possible that the problem only arises when the page the browser is opening has an applet that is not fully visible on the page -- down further on the page perhaps, or just a bit too large? That could be why we've missed this. It looks to me like the effect is only when the applet is not fully visible.
Thomas, please do the following test: Please reduce the size of your applet so that appropriately fits the user's screen. I think you are trying to do that anyway, but it is just a bit too high no matter what I do with the browser window. Then let us test your page again.
Others with Macs. Please try setting the window size of your browser to a smaller window and then open pages that you know should work. Look for a page where the applet is not fully visible. Start tapping, dragging, anything to get the refreshes coming. Do you see the applet freeze? http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm is a fine page to try.
I will put out a version of Jmol that sends messages to the Java console indicating what messages it is getting from the OS and what state it is in.
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900