We have investigated the origin of the large increase in spin-echo decay rates for the $^{77}$Se nuclear spins at temperatures near to $T=30K$ in the organic superconductor (TMTSF)$_2$ClO$_4$. The measured angular dependence of $T_2^{-1}$ demonstrates that the source of the spin-echo decays lies with carrier density fluctuations rather than fluctuations in TMTSF molecular orientation. The very long time scales are directly associated with the dynamics of the anion ordering occurring at $T=25K$, and the inhomogeneously broadened spectra at lower temperatures result from finite domain sizes. Our results are similar to observations of line-broadening effects associated with charge-ordering transitions in quasi-two dimensional organic conductors.