For the first pair, you might like to take a look at this question and the answers. Based on the methodology I used in my own answer there, in A I should like refers to the time of speaking and to have sat down refers to some previous time. In B, on the other hand, I should have liked refers to the same time as the sitting down.
In the second pair, A suggests that the speaker does know the subject, while B suggests that the speaker might not.
In the third pair, A suggests that the medicine made him feel better, while B suggests that he was feeling better before she gave him the medicine.
All of these explanations should be read with a certain amount of caution. Much will depend on the circumstances in which they are being said or written.