Hard to figure what exactly the problem is without seeing your script. Also can you show a long listing of these directories which have their permissions screwed up?
Please post your script as well as a long listing of your /etc/pts directory within
[code][/code] tags.
If you'd rather self analyze:
Sounds sort of like Wave Watch III uses that directory for writing information, be that logs or data. It may be that when you run it as a cron that user permissions are one thing and when you run it directly from a terminal program that the user permissions are your login and that there's a conflict.
Something to do is to echo the environment information to a log file from within your script that's running ww-iii.
Code:
env >> /home/<your-user>/logfile.txt;
And finally check the permissions and ownership for your /etc/pts directory; that's not a normal system directory as far as I know, therefore it may have been created by the ww-iii program; and again it may have been given ownership and credentials via the cron job; and be something which doesn't allow other users to access it.