Doing what? I have run systems similar to yours with jre, and I haven't seen it in any profiling data - so what are you doing when it's running slower?
install suns jre 1.6, enable java in seamonkey and start the browser. That was a major reduction in system performance. only installed the jre to try to attend a webcast on security.
no profiling data, only counting of second blinks in the clock, 15 second load time with no java, 45 second load time with java.
[ multiple jre options is a critical flaw in the java language in my opinion, and until one jre will run every java app as written, it is not usable. ( don't forget, sun broke backwards compatibility with their own jre between 1.12 and 1.14 so there is no true backwards compatibility in java* ) ]
How about using oprofile to measure the difference, and point the code out to someone who can fix it, if it's that noticeable - assuming of course you are not using Java-code to do something, in which case I expect jre to appear somewhere on the profile.
to do that, I would have to have actually been running a java app, not just one with support for java enabled. I didn't get as far as installing the client software for the webcast, as well as actually want java apps on my system. If it requires java, it is of no use, until java is open source, and has one jre with full backwards compatibility I'll not use any java app.
*When I say backwards compatibility, I mean all java apps ever written, which is what Sun broke between sun jre-1.12 and sun jre1.14,( 1998 ) so java has zero backwards compatibility, by SUN's own design.