Well as CLOCK_THREAD_CPUTIME_ID is implemented using rdtsc it will likely suffer from the same problems as it. The manual page for clock_gettime says:
The CLOCK_PROCESS_CPUTIME_ID and CLOCK_THREAD_CPUTIME_ID clocks
are realized on many platforms using timers from the CPUs (TSC on
i386, AR.ITC on Itanium). These registers may differ between CPUs and
as a consequence these clocks may return bogus results if a
process is migrated to another CPU.
Which sounds like it might explain your problems? Maybe you should lock your process to one CPU to get stable results?