By 'manually forced' I assume you mean you ran the scripts directly (not slapping the display around or threatening to strangle the keyboard, right?). Running a script directly means it runs in a different context - different user, different shell environment - and that is probably the source of the different outcome. The scripts are apparently completing their tasks, so this looks like a problem with log-writing; different behavior from different users/environments tends to imply permissions issues, though that's not ironclad.
You might look at /etc/defaults/periodic.conf to see if the _output paths have somehow gotten modified. on my system (10.6.8) I see lines like:
daily_output="/var/log/daily.out"
it may also be a problem with environment variables. the temporary log file is created using the code mktemp ${TMPDIR:-/tmp}/periodic.XXXXXXXXXX which (though a bit beyond my unix skillset) produces a unique path something like /var/folders/MU/MUJU0IllGUuyaCnVQMb50U+++TI/-Tmp-//periodic.U2Yktuwoks. Those files a pwned by root so they may be a bit of a pain to delete, but they ought to be deleted if you manually run the periodic tasks.
You should also check to see if there are any script files in /usr/local/etc/periodic/ - that is apparently a folder for script plug-ins, so if you have a script in that folder that's failing it might bomb the periodic tasks near the end of their execution (though one would think that would show up with a non-0 result or a console entry).
Restart your computer in the maintenance partition and run Disk Utility from that context - repair the disk and the permissions. can't hurt, might help, and doing it from maintenance mode gives you your best shot.
Honestly though, this whole process would be easier if you start from the other end. did you install any apps or utilities around the time that this problem began, or delete any files or apps or utilities? It would have been something that asked for administrative permission - none of the files we're talking about can be accidentally overwritten by a user (even an admin would be prompted for permissions). having an idea what caused the problem would make fixing it much simpler.