Welcome to the forum rage! I'm just spiffballing here because Sony does not publish the frequency response of those speakers (they do rate the response of the cd at 2Hz-20Khz...Duh!), but I would imagine that your issue is less a treble control issue than one of an utter lack of bass.
Despite their proclaimed power rating of 250 watts (and that's at 6 ohms), I don't believe you'll ever experience a preponderance of bass on that system, which may well explain your recent perception of a preponderance of treble.
Additionally, your simple 1 bit dac does not sample nearly as much as a 16 bit dac, so there will be a substantial loss of information. I don't know if this directly answers your question, as you wrote there seemed to be a change in sound, most notably, additional treble. Short of a blown speaker (or other damage), for which you could seek repair (but I would not suggest it, the cost would not justify the result), I would not expect very much from this all in one system. Hope that helps.