As others have said 1000Hz is definitely 1Khz, there's no binary maths involved.
and you are correct that the frequency is 32.678 Khz ( click on "key specs" here)
I would suspect that your millis() time is less accurate than the RTC clock frequency. The crystal resonator used on most Arduinos is only accurate to around 5000ppm whereas the stated accuracy of the RTC is 1ppm.