Have you inoculated started culture from solid medium or glycerol stock ? If it is from solid medium than u need to homogenize (beads +culture+vortex, letting it stand for 20min and using supernatant to inoculate for 7H9). you also need to grow the culture in 7H9 with constant shaking and adding 0.05% tween 80 ( to avoid clumps). You can than calculate CFU without clumping issue.

The inclusion of Tween 80 (0.05% v/v) in the 7H9 growth medium can reduce clumping of MTB in broth. Worth running another assay in parallel with CFU counts in ascertaining MTB viability e.g. the resazurin microplate assay (REMA).