Okay, it looks like the method that Mac OS 9 uses to preserve resource forks on PC drives isn’t compatible with Mac OS X.
Hopefully the old computer has DropStuff or something similar on it (most do). What you’ll need to do is compress the files before you put them onto the flash drive, and then decompress them again once they’re on the new computer. It’s the exact same process as if you were sending them through the Internet, for the exact same reasons.
If the two computers are next to each other, you could alternatively network the two of them and send the plug-ins through file sharing. It may even be possible to recover the resources from the RESOURCE.FRK folder, but transferring compressed files would be a lot simpler.