2 weeks after culture of apical bud in proliferation media (MS medium) with BA or other cytokines in vitro, it starts huge amounts of rooting till the end of the process.
I think you should perform a bioassay in which you try various concentrations of the phytohormones that are using. As the response from your explant depends on the balance between auxin and cytokinin in the culture medium but not forget that the explant perse has certain concentrations of phytohormones which are what determine the answer.
You have mentioned that rooting occurs in the presence of cytokinins, which indicates that the endogenous concentration of the auxins is quite high. You may try to increase the concentration of cytokinins, provided that the fidelity of the resultant propagules is retained (which you can ascertain by observing culture response and using molecular markers). Also, the strength of MS salts plays a vital role in the root induction process. If you have used lower concentrations of MS salts, rooting is quite common. Further, there are references which suggest the role of nitrogen source on rooting. So, you may also try altering the nitrogen source and see if it works.
Dr Ajit Arun Wamen's openion is correct.This is mainly due to endogenous auxin level.Further CKX(cytokinin oxidase) enzyme also play important role in degredation of cytokinins.In your case,you just increase the concentration of cytokinins and completly remove auxins from the medium.Higher concentration of cytokinin will reduce the shoot height.