Hi Tin,
I don't think a PC-side encryption program would be able to affect microSD card operation - the Teensy 3.5 microcontroller interfaces directly with the card without involving the PC operating system.
Is it possible that the problematic PC has multiple copies of Bpod in the MATLAB path? The RotaryEncoderModule class that MATLAB is using could be an old copy that somehow has path priority. To determine this, run "which RotaryEncoderModule" at the MATLAB prompt, and ensure that the path to RotaryEncoderModule.m matches the repository you installed when upgrading to v1.64.
You can also try a command line test of microSD capture and readback to constrain the problem. At the MATLAB command prompt,
R = RotaryEncoderModule('COM3'); % Where 'COM3' is the correct port
R.startLogging;
%
% -- Move the rotary encoder to capture some position data
%
R.stopLogging;
Data = R.getLoggedData;
clear R
Please let me know if these yield any results!
-Josh