I'm having a hard time visualizing the problem from your description. However, I think that what you're looking for is the 'commit record' script step. This updates all relationships, and should cause the portal to refresh. If you don't want the user to have to click a button to commit the record, you can apply it as a script trigger on the field that is not updating.
If that doesn't work, please post a screen shot illustrating the problem so that I can understand it better.