The single ended output will sound a tiny bit better - unless you have an amp that will only accept a balanced input. Then the balanced output will sound better.
If your amp has both SE and balanced inputs it may itself sound different from each input. You just have to smoke it and see.
Doc, I have two systems and both have the balanced and SE option. The distance between the pre and the power amp is about 3m and for this I have to use a 4m long cable. I have compared the sound and the balanced is significantly better in this long run. I'm using unshielded Kimber balanced cables.
My concern is more to the outputs of the Beepre itself, as I understand that there are capacitor and resistor in the balanced out line. Would it, because of the additional components, affect the quality of the sound. That is the reason why I asked for an A-B comparison of the two outputs, out of the users experience. I guess there is no better place to ask about it at this this forum, isn't it?
If I don't have the SE option on the power amp side, as you mentioned, it will make life easier, of course
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I have the Beepre high on the list, that's why I want to know more about this pre amp. But I guess, again, as you mentioned, I'll have to find it out myself later once the Beepre is ready. But using SE connection means changing the lay out of my listening room radically, and whenever possible I'd like to avoid that.