Remember that how you perceive things might be different then how he sees them. I notice with myself I make things into a much bigger deal then they really are. Also, remember he is your boss. That is it. Not your friend, not your confidant, nothing. How I have to look at things with my job is my management team just wants someone that will come in and do a good job, no drama etc. Since I am a recovering addict, single mom, need to take time off when kid is sick, need to leave early to pick them up etc, I raise a flag. So in my mind I get insecure about things, and want some feeling that things are okay by my boss. But I am not going to get that. But, I have to know that inside i am doing the best I can do. Kids first of course, but job has to be okay since I need the income.
Sometimes we need to take our thoughts and insecurities and realize its not that big. You are doing a great job, and he should've never said that to you, but you admit you had a lot on your plate. A LOT. Just like him saying he was surprised you came back. That is not what you wanted to hear. That is like at my work so many of people say 'are you okay' instead of 'how are you' (they are from other countries) well I assume I don't look okay, or whatever. But that is just their way of asking how I am??? So odd to me.
Honestly, know you are doing a good job, keep your head on straight, keep your head up, and turn to us when you need to vent! We are proud of you!