If you have tapped on your negative emotions and gotten to a zero they may very well be gone. If they are gone then they probably are not suppressed. Did you test to see if you could feeling the emotion again? If they return it may be because there was another aspect to the event.
For example I may be angry for my sister not listening to me, so I tap for the anger. And then I still have strong emotion about it and realize that she calls, doesn't listen and so I have resentment for her calling and taking up my time as well as anger. If I get rid of both of those and don't feel upset with my sister any longer, at first it may feel flat or as if something is missing because I was used to the disruption in my energy system surrounding her and her calls. It may feel empty or I may feel as if I am not myself but since I am not yet use to the calm feeling, it seems unnatural to me. It just means that the EFT is working, it is not brainwashing and a new self will emerge...one with more inner peace. (Note: I may have to tap again if she calls again and negative emotions get stirred up again. This doesn't mean that the EFT didn't work, it did. The negative emotion happened again. But as I use EFT for these events they are not as likely to be as upsetting.)
That said I have noticed that some people like the strong negative emotions, even feel like they need it to suit some purpose. I know one young man who did not want to get rid of his anger. He thought he needed it to play and write his rock music and so he was determined to hang on to it.
At times change in itself is uncomfortable. We are not where we were and we haven't arrived at the place we are headed and so we are in uncomfortable sometimes undefinable place "outside of our comfort zone." You may want to tap for "Even though this shift in my feelings is uncomfortable and I'm scared that I'm brainwashing myself, I deeply and completely love and accept myself."
I don't think what you are feeling is unusual, its just that the change may take a little getting used to.