Well, I wasn't getting those discrepancies. So I don't know what to tell you.
At most I was having issues with being a year off - but you can get that from confusion about end of year numbers versus start of the next year numbers.
I was only working with the data, as my Numbers program couldn't import the formulas. I had to jump through some hoops - renamed the file .htm, opening in Safari, and then copying the data and pasting it in my spreadsheet.
I was mostly working with the spreadsheets generated from a given starting year, not the entire data set. And those matched the graphs displayed for the %remaining portfolio scenarios.