I disagree that you are being oversensitive or are overreacting.
I have some experience with workplace changes and with HR (but I am not an HR professional myself, just have worked with them).
While you absolutely DO need to consider, every single day, that hormones certainly may play a role in making you touchy -- do not just let people dismiss your discomfort and worry as "just hormones" here.
What others below are not seeming to notice is that while you were gone two things happened at work that have nothing to do with you or your hormones:
Your office hired five new employees (five at once would be a pretty big change in most offices) AND the project manager suddenly began being much more involved day to day than had been the case previously. The PM's new role indicates that possibly the project manager has been told by his or her boss to do so, and that may mean the PM is in some hot water with HIS own boss -- that is nothing to do with you but the result is an angry and fearful PM who will now lower the boom on everything to make his own position stronger.
You did not do the right thing in two ways:
First, you did not establish, clearly, formally and in writing, your new schedule. That should have been done up front and before you took even an hour of flex time, and your PM, your PM's boss and HR all should have signed off this written change.
Second, you worked at home for a whole week without even clarifying -- not even verbally -- that doing so was approved. Your mistake, and you need to own up to it. While you were doing that it gave the others a lot of time to talk about why you weren't in the office and to wonder about which days you were supposed to come in.
Do you notice that both those things have nothing to do with your child care arrangements or your hormones? Those are workplace issues. You came back into a changed workplace, with new people in the mix who do not know you and probably don't care much about your personal situation unless it affects their own work schedules and workload, and you also came back to a PM who may have some issues of his own with his bosses.
So what do you do now? You prepare, first, and script out what you want to say. You write out your proposed flex schedule. You meet with your direct boss and say that you and he need to formalize the schedule to get it all correct and legal. Don't let him make it just verbal or say "let's just see how it goes week by week." You and he need to set a schedule, period, and you can sell it as "The other employees need to know my schedule too, because we all interact, and it will make their jobs easier and be fairer on them to have a schedule set at least by the month so we all know what to expect." (Does your workplace have a formal work at home policy or was this all just casually OK'd verbally? If the latter - that's bad, and you could be told any moment "You must now work at the office full time, regular hours.")
Be professional when you see the boss. Do NOT mention your child or your care or your husband. Say you are glad to be able to change your schedule and want to be sure you do it right. If you need to, say that you were unclear about the hours when you worked at home that whole week and admit that you should have formalized it before you stayed home.
Do not complain to HR about remarks unless they are at the level of being harassment -- and what you describe isn't. There may come a time when you have to formally challenge harassment (nope, not now) or more likely challenge treatment relating to your schedule. Reserve HR for those things.
As for the questions, I agree with you that if folks are striding up and without preface or other comment, just saying, "What are your child care arrangements?" that is not just friendly interest in how the new mom is doing, as some other posters see it here. I would wager that you now are seen as causing others more work due to your request for a flexible schedule. Be aware of that view of you, and ensure that you are seen to be working above and beyond, and that you want a written schedule so that these coworkers know what to expect.
When people ask about your husband or your baby in ways that seem intrusive, smile a big smile and say, "The baby's doing great" and don't answer specifics. I suspect that some workers don't understand why you need a flexible schedule and work at home if your husband is home full-time with your child. You may get someone asking directly why you need this schedule if you have dad at home all the time. Deflect questions and focus just on work. When you are AT the office you need to spend that time being seen as super efficient and focused anyway so don't let discussions get into the topic of home arrangements; try, "Some issues make it necessary right now. OK, this report here is due next week; today I"m going to complete X and Y sections; when will you have Z ready...." Move the talk always to specific work tasks.
Do NOT get into "I don't think they have a clue about how they made me feel." They will label you the hormonal, emotional new mom who isn't really up to work. Be cool and professional. You returned to a changed workplace and so can't expect coworkers or the PM to be the way they were before. Protect yourself and your new schedule, admit that you were not clear on what to do earlier, and formalize it while emphasizing that "this is so that everyone knows where I am and when, and so I can do my best work."