Explain same encryption time for two files of different sizes
Modern computers are quite fast, and modern cryptographic algorithms are quite efficient.

Most computers benchmark hardware accelerated AES in CTR mode well above 1GB/s, which would be a fraction of a millisecond for a 100KiB file. Since the standard system timer generally runs at 1ms intervals, the entire encryption operation ([file data] XOR [AES] XOR [Pad]) will take less than a single timer 'tick' to complete, and they will report the same completion time.

I would expect files up to 3 MiB will take less than 1ms to complete on computers made in the last 5 years, if the timer is started after the file data is read from disk, just prior to encryption.

Try using a much larger file, at least 1 GiB, in order to gauge the performance of the system. Also, Windows offers a high resolution timer through the kernel, if the hardware supports it, offering sub-microsecond accuracy. If you try to repeatedly measure very small time windows, they will vary greatly if there are other processes using the same CPU core.