|"the folder does contain over 1000 files, but that shouldn't matter right?"|
It probably takes more time to copy more files than it does to copy fewer, but that alone doesn't account for the difference you're seeing, if it's the same flash drive.
USB 2.0 has a maximum theoretical bandwidth of 480 MBit/s = 60 MBytes/s (8 bits per byte), or 48 MBytes/s (10 bits per byte; 8 for data, 2 for "overhead" - all SATA hard drives use 10 bits per byte when transferring data) but you never get that in the real world.
You're fortunate if you get 3x MBytes/s.
"The System always reserves some USB bandwidth for it's use. For Windows look here:
Device Manager (devmgmt.msc)
Universal Serial Bus Controllers, untree this (click the plus sign)
Select any of the "Blah blah blah USB Universal Host Controller / USB2 Enhanced Host Controller"
Right Click > Properties
Advanced Tab (at the top)
Most..." operating "...systems today reserve 10% of the bandwidth "
NOTE - the "Enhanced" Host Controllers listed there are the USB 2.0 (or USB 3.0) host controllers. If you don't see any "Enhanced" Host Controllers there, the built in support Windows has for USB 2.0 (or USB 3.0 ?) has NOT been installed in Windows.
If you have installed Windows from scratch, after Setup has finished, it has only USB 1.1 support installed in Windows.
The USB 2.0 (or USB 3.0) support is NOT installed in Windows until AFTER you have loaded the main chipset drivers for your mboard.
Though USB 2.0 supports data transfer rates of slightly better than 30 MB/sec, modern Flash memory chips can't yet match those speeds.
The max data transfer rate of a flash drive varies greatly depending on which circuitry (chip or chips) it has. The faster the circuitry can run at, the better result you'll get.
Older flash drive models have lower data transfer rates.
E.g. A comparison of recent and fairly recent flash drive models
The data transfer rate you get also depends on what else the operating system is doing at the time. You can't compare data transfer rates unless that's the same.
If the hard drive partition Windows itself was installed on is too full, that will slow down everything in Windows. That partition should have about 10% free space or more.
There are many other reasons for Windows running slower than it once did, and if it's runnig slower that will affect max data transfer speeds.