wvmarle:
The clock of the Arduino is not perfectly accurate, that's one error.Your signal is also probably not perfectly accurate, that's another error.
Together they add up indeed - to a whopping 0.15%! Do you really expect even better accuracy than this on anything but carefully calibrated lab equipment?
The issue is that the Uno doesn't use a crystal for its clock, it uses a ceramic resonator, which are very
poor timekeepers. Standard crystals give +/-30ppm or so accuracy or better, not the +/-5000ppm of a
resonator.