I have owned the STP-SE for almost 3 years now and there could be a few things going on.
The first question I have for you is what amp are you using. The STP-SE likes an amp with a high input impedance, 30K or more I'd say. The best experience I have had with it is using a amp with a 97K input impedance and my current amps, the first gen wyred sx-500s which have input impedance of 100k. I have tried to use two amps with low input impendances one was 10k and the other was 4k and the result was distorted highs and a uncontrolled bottom end. Treat the STP-SE like a tube preamp when looking for a amp to match. The higher the input impedance the better.
The second piece of advice I'd give you has to do with your power distribution. I have had wildly varying results with the STP-SE in different power configurations. A couple of things remain consistent though. Don't plug the STP into the same conditioner, surge protector etc with high current equipment like amps or flat screen tvs. I have done this before and it resulted in a similar sound to what you described. The best success I have had (and my current configuration) is that I have dedicated a PS audio Ultimate outlet to just the STP-SE. If you do have the STP plugged into the same conditioner as your other equipment I would unplug it and plug the STP directly into the wall and see if that makes a difference. If it does then you are having the same issues I just described and just need to separate the pre from the rest of your gear. It just doesn't seem like it wants to share. Just get it a separate conditioner and you should be good to go.
The STP-SE is a fantastic pre and I will never sell mine. To me it is worth selling equipment to get some that match well with it than vice versa.