Hi there! In the last two months, I've gotten certified for Reiki I and II. After my very first Reiki treatment, which I took maybe two weeks prior to Reiki I, I was in a really weird, uncomfortable mood for the next day, but then the day after that, I felt better than I had for months! I was in an amazingly great mood, and it lasted for the rest of that week. Similarly, after my Reiki I certification, I had the odd experience of old emotional wounds that I rarely think about randomly surfacing and nagging me until I was able to come to terms with them.
I think it's just part of your personal commitment to heal, which got jump-started by the Reiki energy you received in your treatment. I've been reading books on energy healing by Barbara Brennan, whose premise is that energy preexists matter, and that it's ultimately stagnant personal energy caused by emotional and spiritual distress that causes physical illness.
If that is the case, I think that Reiki travels through your energy field on its way to your physical body, and works in conjunction with the energy field primarily and the phsyical body after that to initiate healing. So now that you have Reiki lingering in your energy field, it's going through and sweeping up various bits of emotional and spiritual baggage, which has to surface and be dealt with before it can dissipate.
It's similar to a physical detox, where you feel worse before you feel better, except it's centered in your emotional energy. More Reiki treatments will probably help a lot, but maybe taking some time alone to meditate, feel the emotions surface, and consciously let go of them will help as well. It sounds like this treatment could be the catalyst to a wonderful period of emotional and spiritual development for you.
In any case, do keep in touch with your Reiki practitioner, or get in touch with another energy worker for some extra support.
I hope that helps a little bit, and if I can answer any other questions about Reiki for you, I'll try! Just keep in mind that I'm rather new at this.
In fact, if you'd like, I can attempt to send you some more Reiki long-distance to help you out. PM me about it, if you'd like, and I'll do my darndest!