Did you verify that the disk is indeed formatted with NTFS and not FAT32? Win 7 Disk Management can tell you that.

Don't know about Crystal disk benchmarks. I would try something simple, how fast can the DB be read?
>copy yourDBname.sqlite NULL on Windows, NULL is a reserved file name that means "the bit bucket".
See if there is any difference between the computers...

Perhaps some experimentation to see what kind of cliff you are hitting might be interesting...Make a DB 1/10 the current size and benchmark that - see if the 400 MB file compares ok against the other machines or not.