research makes me feel a bad scientist

I am now in the I hate my work phase. I have seen it happening in many of my colleague PhD students, and apparently it is my turn now. The problem is that I had everything done for the final final version of another chapter of my thesis, when somebody said.. well you have checked everything, right? And I said yes of course. And compulsive as I am I ran all analyses again. Finding that a script was malfunctioning all the time, leading to one column of data that needed another step of processing. Having repaired the script my data is "all different now". Well it is mainly the same, only two results flipped. The rest is the same.... So the chapter can remain somewhat the same, but the main conclusions, that we measure what we measure is "slightly" different. Let me try and explain: I have designed two compounds, Z and Y. There are two logical compounds Z and Y can react with, A and B. I expect Z to react with either only A or with A and B. And I don't care if Y reacts with A, B or A and B. I apply bonferroni because I do a lot of reactions. There is some discussion about why applying bonferroni, some co-authors say I am over zealous applying it because nobody does that. The latter, I think, is a bad argument, which I chose to ignore. What we found was that Z did react with A and B, and Y reacted with B. Due to Bonferroni, one finding I can not explain (a reaction with substance V), is no longer significant, so I don't have to think of any weird explanations why on earth there is this weird reaction with substance V. Situation now in the correctly calculated data set: Without Bonferroni: Z reacts with A and B, Y reacts with A and B, and Z and Y react to each other (explainable). And substance V does its weird thing as well (unexplainable?). With bonferroni: I loose the weird substance V again, jay! However, I loose my precious Z reaction with A, while the (completely legit) reaction with B remains. Z only reacts with B. Y reacts with A and B. I wish I wasn't so compulsive in this phase, or would have been more compulsive in an earlier phase in the process. Now what. I thought I was done with this chapter. And now I guess I need to figure out a way to either integrate substance V in the manuscript. Don't know how... Or I have to think of a way to explain why Z still is related to A, only there is no significant reaction. Don't know how... Tomorrow I have a meeting with my co-promotors. I feel like a lousy scientist right now. I am so afraid they will think of me like that as well.... Why on earth havn't I checked the complete file in an earlier phase. Why!!! Bad, bad scientist!