Part of the problem may lie with the adverb yet. If you remove it, you can see that the two constructions are opened up to slightly different interpretations:
- It seems you didn't leave.
There is some suggestion that the person is not going to leave, for whatever reason.
- It seems you haven't left.
This is more open-ended. The person might leave, or might not. The only fact in evidence is not having left. There is almost an implied yet at the end.
If the above shadings are accurate to your inner listener, adding yet would merely enhance the unfinished nature of 2 while work at cross purposes to 1, possibly the point of negating it. That may be the slight discordance some of us hear when adding yet to 1: its finality is taken away.
Note that either case could easily go the other way and still be expressive and grammatical. We're talking about fine shadings of meaning, superimpositions on a somewhat arbitrary structure.