Time delay estimation using ultrasound
The transient edge or pulse shape of a tone burst represents a modulation.  The resulting modulated signal will contain frequency components higher than the tone frequency.  Thus you may need a sample rate much higher than just over 2X the tone frequency to reproduce a waveform accurately enough for cross-correlation to match the edges of the pulse envelopes.  This is likely true for your low tones and for voices, where the sample rate can be 10X to 200X higher than the tone or forment frequencies.

Filtering out frequencies just below the tone carrier can also remove any lower sidebands of the modulation, thus likely increasing the error in envelope matching by cross-correlation.