I am not sure if it is the right approach to solve a technical problem by asking why users are doing things the way users a doing things. Anyway I will tell you, so we can get back on track 
Using Windows 8 with your start menu in a professional context, i need to work with a bunch of files of the same file type - like office documents - every day.
But then sometimes one wants to "clean up" the working space, but there are some files that are needed regularly, e.g. for administration stuff. These files are pinned, that's why Microsoft invented that (think so). And this is why Windows 7 start menu probably behaves exactly that way.
And now I thought the intention of Start8 was or is to bring exactly this functionality to Windows 8 - tell me if i'm wrong.
By the way I am not sure, if the problem is a deleted registry key (the "system" still knows about the pinned files "somewhere", they are just not displayed in Start8).
So in order to solve this - after deleting the recent file list - I have to open a document - doesn't have to be a pinned one, just a document for the relevant application (in this case any spreadsheet file for Excel) - to get the pinned files visible again, additional to the one I just opened.
So now everything is said and it would be so fantastic, if Start8 would soon behave like the standard start menu of Windows 7.
Thx in advance, you are the man .