Sony 900ES SACD sound vs CD - Help

I now have a little over 120 hours on my 9000ES DVD. Here's the problem: When I use the Sony as a transport (The digital output fed into an MSB Link Dac 2) the sound quality is MUCH better than the Sony supplied SACD music played through the SACD internal decoding circuits and output form the analog outputs on the Sony.

How can this be? I thought the SACD was supposed to be much better than the CD. Is it possible that the SACD circuits need much more time to break in?

The Sony when used as a transport is almost as good as my SimAudio Moon Eclipse cd player (when also used as a transport) which has a floating suspension.

I have the Sony on a magnetic levitation system which I designed that floats it 1/4 to 1/2" off the shelf.
This isolates the transport and circuitry from low frequency vibration. The result is: better bass, more open midrange, and clearer highs.

I just don't understand why the SACD part of this doesn't sound as good as everyone says it does. Maybe the sampler sacd is very good?

Any ideas??