But I would recommend using XP's Task Scheduler to simply schedule it to
run with the appropriate flags.

As for "because the files were all clustered together", that simply
creates more need for more defrags than is neccessary.  Fragmentation
begins to happen within the first few writes to the disk, where as when
there are spaces between the file sets, the OS can more quickly find a
place to dop a file.  Remember, the registry is being read and written
to constantly, so even if you don't create files, fragmentation is going
to start happening.

I never heard of JKDefrag but if it's any good it will have options for
putting things on the beginning, first, mid, last, and the end of the
sector lists.  Else it's not much good if it only does what you
describe.  In general, IMO, using a 3rd part app to do what XP can do
well natively is just adding more opportunity for problems and
corruption to occur both on disk and in memory and in the registry.
 Perhaps you should research the registry and its use a little?

HTH