Level 41 Jedi Knight here. Affection metre for Kira Reads 8978/10000.
I took the dark side flirt option earlier in the story and have had the same issue of no interaction with Kira since then. The issue hasn't been cleared up for me with the latest patch.
Can't interact with Kira on any planets nor on my personal spaceship either so if there has been a supposed 'fix' then it hasn't worked for me.