It is nice that the Kobo is fast (and that sort of proofs the PC end of the USB), but we are troublshooting the Sony by performing test steps
It's USB could be poor or not playing nice with the PC (My first PEz would Fault if I allowed USB2
was out of spec hardware.)
People tend to equate 'Freezing' with
too busy to respond.
Scanning a device for books and MARKING them in Calibre is intensive use of the CPU and USB port.
If you interrupt this, it has to start over the next connection.
There may be a Sony driver configuration setting to limit where the scan phase looke, otherwise... All storage gets examined.