Error Log Creation Issues

This is going to be quite vague until I know for sure what information is needed to resolve this, but we are having some problems with output logs being written and saved for the vast majority of our scripts. The logs for a fraction of our total scripts, maybe less than 2%, are not being written, or are being written and quickly overridden or deleted very shortly afterwards. We are running the most recent version of Screen Scraper and Java, how else can we help get to the bottom of this? Thanks guys.