It's probably not java (as in the java VM on the machine), but javascript in the browser.  I have noticed that firefox's javascript is noticably slower on linux than on windows (both 64-bit and 32).  Check out for example digg.com (a site that makes extensive use of javascript).  There is a noticeable performance difference. 

... HH

On 12/29/06, Duncan <1i5t5.duncan@cox.net> wrote:
"Mark Knecht" <markknecht@gmail.com> posted
5bdc1c8b0612291445h1c927ecag3cfdf19f134a6e28@mail.gmail.com , excerpted
below, on  Fri, 29 Dec 2006 14:45:37 -0800:

>    Note that if this was just Flash on the front page it would be no
> big deal. However I think there may be additional issues around the speed
> of Java once you log in and get inside the web site. That is what really
> matters and it's very slow on this machine.

What Java are you using?  When I switched to Gentoo I decided I didn't
need Java enough to override its being proprietary, so I don't have it
installed here and haven't had it installed on Gentoo at all.  However,
back on Mandrake, I noticed Java was /dreadfully/ slow at times on Linux.
IIRC, I was using kaffe JVM at that time and attributed it to that, but I
was trying to run broadbandreports.com's Java based speedtest applet, and
it was simply too slow executing to produce anything even /close/ to
reliable results.

So it may be the JVM or something Java related, rather than flash or
whatever.

Happily, now that Sun is GPLing Java, I should be able to merge a decent
and freedom software based Java one of these days. I'm looking forward
to it!  =8^)

--
Duncan - List replies preferred.   No HTML msgs.
"Every nonfree program has a lord, a master --
and if you use the program, he is your master."  Richard Stallman

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Harry Holt, PMP