I don't think I've ever heard someone say "you're a good listener" as a backhanded compliment or subtle insult. If you're actively listening then you are a good listener and if someone else has something they want to talk about then there is no problem with letting them lead the conversation.
Kyoto dialect is culturally full of them, apparently, with the two examples that spring to mind being "That's a nice watch you have (take a look at it and realize you're eating up my time)" and a "You've been getting better at the piano (which I shouldn't be able to hear you playing, keep it down)."
Meanwhile, it's been a minor plot point or drama point in multiple series I've seen that the generally accepted convention in Japan is for conversations to be a back-and-forth like a game of catch, so if someone monopolizes the conversation (or, contrariwise, has to do all the talking), the other person may feel put out.
That's not how she meant it, obviously, but Japanese cultural norms can be pretty ingrained, to the degree that I've seen more than one story about non-native speakers taking up the role of Gaijin Who's Clueless Enough To Simply Ask The Question We Need An Answer To/Say The Thing Nobody Wanted To Tell The Troublemaker (or fall into it). People in anime and manga get in their heads about stuff like this for a reason, after all.