This sounds like a classic case of system load to me.
When you read/write something to/from a drive, it needs to lookup file information. However, that file may be fragmented, in different locations, or even organized.
When you copy something from your drive to a USB, you have to read a (potentially) fragmented file and then re-write it to another storage medium. With some systems (read EXT), it is often faster than other systems (cough NTFS cough). Also, if you have a bad processor, it wastes cycles for other things trying to copy things over.
There is really nothing you can do to solve this issue. There are workarounds, however:
- Defragment your hard drive.
- Use an EXT formatted flash drive where possible.
- Install more memory as a "cache" space.
- Use excess memory as a ramdisc.
- Use a better USB protocol.
- Upgrade your processor/PC.
- Get an SSD.