Hi Mike
I have seen the same and I think this is due to recent in Javaapplet security issues and fixes and the way browsers (esp IE 9) handle these. Can be tricky to fix as it depends on the particular version of browser and Java locally installed (Windows update and Java update policies?) and the version of Jmol on the server. You could try updating to the very latest versions of each, though it may not fix things. IE 10, or recent Firefox or Chrome all work for me.
If you can wait a few days, I should have a new, JavaScript/HTML5 only, version of the filter based on JSmol. JSmol *is* Jmol but recompiled as JavaScript. Incredibly impressive development work by BobHanson and colleagues.
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
As well as avoiding Java security issues, JSmol should work on platforms that don't support Java.
I'll post again as soon as I release the updated Jmol filter (JSmol filter) code.
