You have not mentioned which staining technique you are using in this case. Have you tried to do it without hydrolysis? Sometimes hydrolysing the roots separately hinders the staining of roots. It happened with me. I used 9:1 2% Propiono-orcein: 1N HCl mix and this helped.
Thank you for your attention. I hydrolyzed the root tips in 1 N NaOH at 60 °C for 17 min, and after washing the roots, I used aceto-iron-haematoxylin to staining the chromosomes.