Hi Niamh,
CHIRP, as provided by your example CSV file, is working as expected and as designed.
1,GB3AP,145.6125,-,0.6,Tone,94.8,94.8,23,NN,NFM,5,,,,,,
2,GB3AR,145.7,-,0.6,Tone,110.9,110.9,23,NN,NFM,5,,,,,,
When Tone Mode is set to Tone (as shown above), only the Tone column (rToneFreq in the CSV file) is used. Any value in the ToneSql field (cToneFreq in the CSV file) is ignored. If the Hide Unused Fields setting of CHIRP is enabled (the default for new CHIRP installations), the ToneSql field will be blank. The radio will use the CTCSS tone from the Tone column as the TX CTCSS tone. Carrier squelch will be used for RX.
1,GB3AP,145.6125,-,0.6,TSQL,94.8,94.8,23,NN,NFM,5,,,,,,
2,GB3AR,145.7,-,0.6,TSQL,88.5,110.9,23,NN,NFM,5,,,,,,
If you want a value in the ToneSql column, then you must set the Tone Mode to TSQL (Tone in the CSV file) as shown above. You can populate the rToneFreq field in the CSV file with the default 88.5 or the same value as the cToneFreq field. It doesn't matter either way. The radio will use the CTCSS tone from the ToneSql column (cToneFreq in the CSV file) for both the TX and RX CTCSS tone. CHIRP will ignore the value in the Tone column (rToneFreq in the CSV file) and the Tone field will be blank if the Hide Unused Fields setting is enabled.
For more details about how the CHIRP columns are used and selective squelch columns affect one another, take a look at these reference guides.
"CHIRP Programming Reference":http://kc9hi.dyndns.org/uv5r/programming/CHIRP%20Guide.pdf
"Understanding CHIRP's columns":https://chirp.danplanet.com/projects/chirp/wiki/MemoryEditorColumns
Jim KC9HI