I agree with Reubent, using a preamp is not always an asset. In fact, sometimes it is a downgrade.
Jjmali, the poster is not using a passive preamp. The preamp in the ML 39 is based on the ML 380 active preamp. Wes Phillips (who's opinions I respect) had this to say in his review of the ML 39 CD player:
"You think your preamp is transparent? You're probably wrong. I knew this, of course, but I've never heard a CD player's variable output that wasn't more colored or coarse than a good preamp. Not even the best of 'em. So I was stunned by how good the '39 sounded going straight in. It was fast and clean—and more. More depth, more dynamics, more detail, more air... "
So we can rule the preamp out as the culprit, with a fairly high degree of certainty. There are other more likely causes, as I outlined in my previous post.
Since a couple of other posters questioned the cable choices, that appears to be a good place to start...