Oh, I see. My experience with piliated strains is circumscribed to making mutants via transformation with recombinant plasmids (N. meningitidis, piliation assessed beforehand via negative staining/TEM). I never noticed clumping; this was on BHI 5 mL liquid cultures supplemented with 10 mM MgCl2 inoculated at fairly high OD and grown under shaking. Transformed colonies were never clonal, serial streaking (at least twice) was required to obtain pure cultues, but I alwas attributed -perhaps mistakenly- this to the fact that they appear as diplococci.
Perhaps the clumping you observe has to do with the medium? Sorry I can't be of help.