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Saving all macros and loading them as global macros in the chained project is not a good idea. Global macros take precedence over system macros, so any system macros in the parent project's 'all' collection will become global macros in the child instance, overriding the true system macro values there.
It would be much better to narrow down the original problem to a reproducible case that we can investigate here. Using v6, you could add project-level step script events to log the problem macros before and after each step to isolate when they are changing or getting deleted. In v5, you would have to add the script code to each step's script code (you can multi-select steps and edit step script, but it will replace any existing script code for those steps).
Also, please post the info from Help | About | Install Info. Thanks.
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