The death of homunculus does not affect its intimacy.
The only thing affects the homunculus' intimacy is the feeding.
feed it between 11- 25 for the best intimacy point, which is +1 point
Just don't feed it below or above those numbers and you'll be fine
EDIT: I think that's normal.
It should become shy soon, after a bit more feeding.
My pet became shy around 38 or so, if you properly fed the homunculus that is