The "problem" with the linux client is that it was compiled with gcc. Meanwhile, the windoze client was specially tweeked and compiled with the Intel compiler (Intel, of course, being a BIG sponsor of SETI@Home 😉 )
HOWEVER.... there is NOW an Intel compiler for linux. 😀
So... Will the the linux porter request to recompile the linux client so that it runs just as fast as the CLI?
(/me won't hold her breath... *rolls eyes*)