In all the cases, I had my main copy of Pages running on a document I wanted the script to reformat. Instead, sometime after each reboot, the script would run a copy of Pages from a system disk I had created and tested, just prior to updating my main system disk to Lion.
I also run a copy of TimeMachine, just use the extra backups as insurance. I tend to consider TimeMachine as a way of getting old versions of a document.
I have three physical disks. Time Machine and the backup partitions are kept on separate disks from the main system and document disks. If a disk fails, the backups are on another disk.
After zipping the copy of Pages on the preLion backup, I have not seen the problem again.