You are getting truely strange numbers! The measurement is in
microseconds, btw. Max should stay below 100 for a nanosleep call:
cyclictest -c 1 -n -p 80 -t 1 -i 1000
c = clock select: 0=CLOCK_MONOTONIC, 1=CLOCK_REALTIME
n = use clock_nanosleep
p = task priority
r = use relative timer instead of absolute timer
i = base intervall in microseconds
t = number of threads.
You may try different options and check if it makes any difference.
This might help isolating the problem.
Did you also applied "idle=poll" as kernel boot option?