Yes: disable the Prefetcher.
I don't think that this is a big deal since this effect is only most noticeable after using the monthly script which moves all files around and which you hopefully don't use more often than once a month. The other scripts move far less files, so you likely won't notice a change in the boot time.
But there is also a way to make Prefetch reindex the files after they have been moved: Execute the following command in the Start > Run dialog:rundll32 advapi32.dll, ProcessIdleTasks
This updates the prefetch files but it will also rearrange the boot files if you haven't disabled this specific feature
. This will also happen automatically every three days.