I had the same problem, this is my solution:
$] uname -a
Linux ******* x86_64 x86_64 x86_64 GNU/Linux
=> downloading a bin :jdk-6u45-linux-x64.bin
=> In my installation location
$]chmod u+x jdk-6u45-linux-x64.bin
$]./jdk-6u45-linux-x64.bin
...
Done
$]cd jdk1.6.0_45/jre/bin
$]./java -version
java version "1.6.0_45"
Java(TM) SE Runtime Environment (build 1.6.0_45-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.45-b01, mixed mode)
It works..
1/ check your server configuration
2/ verify the owner of diretories after unpackaging.
2/ use binary pacquage .bin
Regards.
Richy.