This seems to be a better approach:
library(rgl)
x = rnorm(2700,0,0.6)
y = rnorm(2700,0,0.7)
z = rnorm(2700,0,0.5)
plot3d(x,y,z)
COLS <- rep(NA, 2700)
COLS[c(73:193,409:481,937:1579)] <- "black"
COLS[229:373] <- "green"
COLS[517:721] <- "red"
COLS[757:901] <- "blue"
COLS[1615:1963] <- "cyan"
plot3d(x,y,z,col=COLS)
NA's remain uncolored.