Problems with compare-only with more than 2 sequences

[Liverworks]

Dear developers,

thank you for this amazing tool. I have an issue that I am not completely sure how to describe.

I ran compare-only mode on fastas with three sequences inside. Sometimes the output is as expected - three comparisons seq1-seq2, 1-3 and 2-3. But sometimes I have 1-2, 2-3 and 2-3. So, 2-3 is two times just with different names.

I am not sure why it works like that only for some fastas. If I extract just sequences 1 and 3 and run compare them I get 1-3 as expected and which is different from any output from fasta with 3 sequences.