LimeWire calculates cryptographic hashes for all of those files and stores them in RAM, which speeds up the process of sharing those files if you so choose. This is quite CPU intensive until all of the files in your download directory have been hashed.

Ideally, all filesystems would support rich metadata that would allow LimeWire to store the SHA-1 and Tiger tree as an attribute of each file. However, this is not the case, and storing this information in RAM is a nearly ideal solution for nearly all users.

For most users, this increases the speed with which they can share files and doesn't waste much RAM or CPU time on files that will never be shared. Your situation happens to be an extreme case, and your work-around is easy and effective.