It's really really random.

On one of my accs, 8 red chakra runes in 47k practice pts. (4 were useless tai/nin pen ones, within a span of 5k practice pts).
On my second acc, 2 red chakra runes at 37k practice pts. (with one being bleh control and one being useless injury.)
On my 3rd acc, no red chakra runes at all.