Different results when experiment repeated
That certainly means that this material is not ready for publication.

No matter when the error (is it even an error?) was made (in the initial or subsequent experiment), one first has to figure out why the results are the way they are. From some angle, it is even a blessing that the results are mismatched: it forced to "bake the research" a little longer until it is ready.

I strongly suggest analyzing the experiments setup, experiment procedure, raw data, post-processed results in order to explain what is going on. Maybe, it's worth conducting a third experiment (if it is a viable approach). 

While triple modular redundancy adage does not fit here perfectly as an analog:


  Never go to sea with two chronometers; take one or three.


the third (fourth/fifth/...) experiment might give you some insight into what is going on. And taking only one chronometer—just because it leads to a potentially faster publication—would be a wrong approach.