I agree, this is bug-like behaviour. Like another thread of mine on running cron jobs for my iBook that can NOT be on 24/7, and can not wake at night automatically, I could have some problems soon since an app crashes at least 2 times a day.
I would seriously advise against locking the folder, just because you're interfering with normal system behaviour; I would suggest making sure the periodic scripts are force run at some point.
That said, I'm amazed to see that, in a month, my logs are only 4 kb and 156 kb (/Library and ~/Library respectively).