I expect that all chronographs use a quartz crystal as a reference for their time base. An el-cheapo (under $1) crystal will have an error of only +/-100 ppm (parts-per-million) over a -10 C to +70 C temperature range. A 100 ppm error is 0.01%. At 3000 fps, this is an error of 0.3 fps! So unless there are other errors, the time base is itself is plenty accurate.
It's also possible that there are other sources of error, like variable thresholds in the light sensors, dirt on the lenses, incorrect sensor spacing, etc., that could cause significant errors.
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