When you say (quote) "I then transfer the flash drive back into my Amiga" - what USB interface are you using? Does it work correctly when transferring other files? Have you tried copying the DOpus executable off the flash drive (for example, into RAM: ) and running it from there?
Another alternative that I've always used is DirWork. Older versions (up to 1.62) are just one single executable file and fit easily onto a floppy. Newer versions (up to 2.1) are a bit more complex to install, but have more "bells & whistles".
Also you could try running something like SnoopDOS to see if DOpus is looking for any libraries or dependencies, or anything, which is causing it to crash.
