I installed AS 5.0 on NT4 SP6a IE5.5sp2 and I was not able reproduce the problem you mentioned in your posting.
So I would like to know when you are getting this run time error message.
Is it when you click on the Save button in Tuner or is it when Tuner is being loaded?
Are you able to successfully open each view by clicking on different nodes in Tuner tree like "Package Validation", "Files", or “Registry" etc etc?