I have my options set to move large files to the end of the drive during defrag (Disk Images and Movie Files > 650 MB) which works just fine during a manual defrag. I also have scheduled Defraggler to defrag 'OS (C:\)' once daily at 8pm. However when that scheduled defrag is complete I can see that Defraggler put the large files back in the middle of the drive with the rest, as if ignoring the 'move large files to the end of the drive' option.
There has been one or two queries recently about scheduled defrags, which uses "df.exe" as opposed to "Defraggler.exe". Separate files, but both found in Defragglers "Program Files" folder.
The devs do read these posts, so will probably add this query to the other regarding df.exe picking up the INI file settings.
Sorry I couldn't be of more help, but "df.exe" issues are over to the devs at the moment.