"I'm working on a patch, but I noticed a similar issue in Condition.wait(), which also keeps re-evaluating the "remaining sleep time" based on the current kernel clock, with similar effects."

I see that Lock.acquire(timeout) uses the C function gettimeofday() to recompute the timeout if acquiring the lock was interrupted (C error "EINTR"). It would be better to use a monotonic clock here, but please open a new issue because it's unrelated to nanosleep().

Or did you another bug?

By the way, you didn't mention the Python version. Are you working on Python 2.7 or 3.5?

See also the PEP 418.