[MxxCon]

flashfxp doesn't store data in any order.
flashfxp receives data from a server and then when buffers are full, initiates a flush. It's up to OS to write out data from those buffers to disk in whatever order it does.

just because a file is fragmented doesn't mean it'll always perform slower than a contiguous file. in ntfs some level of fragmentation is natural and there is nothing can be done about that.
furthermore, if you have other activity on that disk, OS might have no choice but to fragment a file.