I'm not able to reproduce this, but perhaps I'm not doing what you are doing. Please explain step by step how you are going from CS5.5 to CS5, and what you see in both files, as well as if any master items that are reappearing were overriden or deleted.
I explain you in detail.
I open the Indesign CS5.5 File and Export the File as .idml and then I opened the file in Indesign CS5. In Indesign CS5 File The Master Page Items are Shown in Layout Pages.
For Example A master Page Items are shown in Layout Pages(This Layout Page is Based on another Master Page)
Hope u can understand this?
I think we need some screen captures of a page as it appears in CS5.5 and in CS5, and a view of the pages panel showing the master pages section.