I have the same problem, but cannot not solve it with the above RewriteCond/RewriteRule.
I am using http://striderweb.com/nerdaphernalia/features/virtual-multiblog/
to serve my to websites ( http://openmtbmap.org and http://www.velomap.org )from the same installation on my dedicated root server.
I have to enable all plugins on both sites, on my main site (openmtmbap) everything works fine, but on my "www" velomap.org site, also if activated and supposedly working, pages are not cached (saying cookie rejected) and users typing adresses without www get shown an error page. If I use the above rules, then people of both my sites get redirected to the www. site mentioned in the rewriterule.
I am not sure if virtual multiblog for wordpress is to blame, but due to this problem I am not able to use W3TC (too much work to disable virtual multiblog for wordpress once setup and create and service two seperate wordpress installations, the new wordpress default multiblog does not cut it for me)....
Otherwise, compared to when I looked up W3TC about 6 month ago, great that qtranslate is now compatible and performance seems to be much better than back then. Now W3TC is more performant than wp supercache plus using xcache (with W3TC using xcache where advised, else using disk/disk enhance only performance is not so great...)