I think I have the issue solved -- at least temporarily.  The note below is a 
second communication from Mr. Michaud.  On the basis of that I have observed 
the following:

        Right click on the Firefox icon to open package contents.
        Go to Contents>macOS>Plugins

In Firefox 4 this folder does not exist (yet) and hence there are no plugins.
In Firefox 3.6 and earlier, there are at least two plugins therein: 
JavaEmbeddingPlugin and MRJPlugin.

Firefox 4 works with my programs; Firefox 3.6 does not.   

I have removed the 2 plugins from 3.6, restarted Firefox and all is now well as 
far  as I can tell.   Testers??

        www.pbays/saintmarys.edu/~pbays/Stereochemistry.html 

        and choose the first menu item that uses Jmol (Comparing Fischer 
Projections)

Phil


Begin forwarded message:

> From: Steven Michaud <[email protected]>
> Date: August 11, 2010 12:46:44 PM EDT
> To: Philip Bays <[email protected]>
> Subject: Re: Java embedding plugin
> 
> Firefox 4 and its predecessors have for some time (on OS X) not bundled the 
> JEP -- instead it uses a port to OS X (done mostly by Apple) of Sun's Java 
> Plugin2 (which mostly runs in a separate process, and has been available for 
> a couple of years (from Sun) for Windows and Linux).
> 
> Apple doesn't say much about their port of Java Plugin2, and (as best I can 
> tell) it's not been officially released.  But it's been included in the last 
> 2-3 Java updates for both OS X 10.6 and OS X 10.5.  You can also "turn on" 
> Java Plugin2 for older Firefox versions by removing the JEP 
> (JavaEmbeddingPlugin.bundle and MRJPlugin.plugin) from the distro's 
> Contents/MacOS/plugins directory.
> 
> Earlier versions of Apple's Java Plugin2 were of very low quality (basically 
> pre-alpha quality).  But the latest versions (available with the latest Apple 
> Java updates) are much improved -- though they still have serious problems 
> (for which see https://bugzilla.mozilla.org/show_bug.cgi?id=554103).  Feel 
> free to try it out -- though you'll find that 
> https://bugzilla.mozilla.org/show_bug.cgi?id=563801 makes JMOL applets 
> more-or-less unusable in FF 3.6.X and below.
> 
> Initially I assumed that the JEP would be obsoleted by Apple's port of Java 
> Plugin2.  But early versions of it were so bad that I began to have doubts, 
> and I started working on a new version of the JEP that works with Firefox 4.  
> The latest versions of Java Plugin2 show more promise, but I've already spent 
> so much time on what I'm calling my "new JEP" that I'm going to finish it 
> regardless, and let users choose which they prefer.  (My new JEP will almost 
> certainly not be bundled with Firefox 4, though it will presumably continue 
> to be bundled with older FF versions.)
> 
> Philip Bays wrote:
>> Thanks.  You should know that, at least through Beta 2, Firefox 4
>> does not exhibit this issue.
>> Phil Bays
>> On Aug 11, 2010, at 11:58 AM, Steven Michaud wrote:
>>> Sorry to take so long to respond.  For a while I was on vacation,
>>> then I was terribly busy with other things.
>>> Turns out this is a bug in the JEP -- a very minor aspect of
>>> SnowLeopard compatibility (or perhaps of Java 6 compatibility) that
>>> I hadn't noticed before.
>>> The access error I see is:
>>> eval ERROR: java.security.AccessControlException: access denied
>>> (java.util.PropertyPermission http.agent read)
>>> I suspect all I need to do is make this property readable to Java
>>> applets.
>>> Philip Bays wrote:
>>>> We are having difficulties with a java applet running under any
>>>> of the recent Mozilla browsers.  I note that the plugin is
>>>> included in all of them and is necessary for the browsers to run
>>>> the applet. But it is unclear to me from your web page that it
>>>> really works on Snow Leopard.   Can you clarify that for me? In
>>>> particular, the problem confirmed by several users in different parts of 
>>>> the country, relates to java cache.  The applet is jmol which displays 
>>>> molecular structures.  From a cleared java cache, Firefox runs fine, 
>>>> loading the applet, and the first molecule.
>>>> If you push a button, and second molecule file is loaded into the
>>>> applet.  Three items now appear in the java cache: the applet
>>>> and both molecule files. If you now close firefox, reopen, and go
>>>> to the same page, the applet loads and the first molecule loads.
>>>> However, the second one throws a java access error.  If you
>>>> remove that second molecular file from the java cache, the the
>>>> page works fine again, until you shut down firefox. 
>>>> www.saintmarys.edu/~pbays/JStest/HTMLFiles/NT1.html There are two
>>>> other files:  NT2 which uses the signed applet and works fine and
>>>> NT3 which sets the threading and works fine. The question I have
>>>> is this: based on your experience, is this a firefox issue, a
>>>> java issue, or a plugin issue, or some combination of the three? Phil Bays 
>>>> J. Philip Bays Professor of Chemistry Department of
>>>> Chemistry and Physics Saint Mary's College Notre Dame, IN 46556
>>>> (574) 284-4663 [email protected]
>> J. Philip Bays Professor of Chemistry Department of Chemistry and
>> Physics Saint Mary's College Notre Dame, IN 46556 (574) 284-4663 
>> [email protected]
> 

J. Philip Bays
Professor of Chemistry
Science Hall 172
Saint Mary's College
Notre Dame  IN  46556
(574) 284-4663

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