Would try to either add glycine to the solution (see S Lee et al Tuberculosis. 82 (4-5): 167-174 regarding electroporation of M avium), increase the level of glycerol to 15%, or resuspend M bovis to 7H9 broth and then add glycerol to reduce clumping

Not sure if this will help, but I have frozen other bacterial colonies in a 50:50 PBS:Glycerol solution before, so increasing the % glycerol in the solution may help.

Thank you Joel and Helene. So hint is to adjust the glycerol concentration.