I have discovered that this happens when these templates are published to servers running very old server extensions. It's best to have at least 2000 extensions.The best fix is to upgrade your server extensions.
If you can't do that or switch hosts then here's what you can do.
Open all the pages on the main level of the flow chart > double click on the nav bars of each page > set to "same level"
Then open all pages on the bottom level of the flow chart > double click on the main nav bars of each page > set to "Parent level."
These templates are all made setting the main nav bars to child pages under home. Old server extensions get confused with that because FP98 didn't have such a setting.
