I installed 6u10 b07 kernel. It installed fine. I waited for kernel to finish before launching the 6u11 online install.
When I tried to patch-in-place to 6u12, patchjre failed with a mismatch error.
6u10 non-kernel online install to 6u12 using patch-in-place worked.
I am guessing that files left by java kernel do not match files installed by the non-java kernel install.