Can you provide all the steps your job does in order as well as the conditions attached to each task? Also, what triggers are attached to this job? Is it just the file trigger or is there a timed execution as well? From reading your posts so far this is what I understand:
Step 1: A program outside of VisualCron downloads the files from an FTP site.
Step 2: Once the files have been downloaded, VisualCron is supposed to start a job (or is it multiple jobs?) that process them.
Is this correct? If so, have you considered having VisualCron perform the FTP actions to download the files? That way once it completes the very next step in the job will be the task that processes them. I have setup multiple jobs on our system where the first step is to download the file then perform a PGP decrypt, or run a program, or archive the file, etc. I haven't experienced any file locking issues when doing it this way.
Regards,
Peter