There isn't enough specific information in your question to give you a definitive answer, but I suspect that you are seeing an increase in the MIC because the copy number of the shuttle vector containing your wildtype allele results in higher expression levels that the single chromosomal copy of the parent strain. 

Thanks John. 

I am testing a gene function and involvement in the resistance to beta lacatam antibiotics. Inactivating this gene reduced the MIC value of the tested strains. To confirm i need to complement with the wild type allele and see restoration of the wild type resistance pattern. I generated the mutants by phage transduction of the transposon insertion to different MRSA strains. I cloned the gene into a shuttle vector then propagated it in e.coli intermediate strain (SA08B) the recombinant vector was then used to transform the mutants and complement with the wild type allele. 

Hope these information will help to get a better answer. Thanks