Transfer speeds
Very small files are transferred at slower speeds, you get more speed with larger files.
The files you're copying are compressed executable files from the Windows 98 setup, and I would guess that your antivirus software (if you have any) also gets between and scans each file for viruses before your WIndows explorer gets a chance to read it.
The flash is also removable, which means Windows may disable read and write caching, because it's not sure if the flash drive will be there the next minute. Explorer copies a file, then waits for the flash drive to say "yeah, the file is completely written on the memory chip, i'm not storing parts of it inside the flash drive controller or ram or anything, it's written for sure", before starting to copy a new file. So after every single file, there's a small pause where Explorer waits for the flash drive to confirm the transfer went fine.
With the other transfer, you have a bunch of caching, the network card driver buffers some data, the operating system will buffer some, and will lie and say the data was written to disk before the writing process is actually complete. It also seems to be bigger files.

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