Check the variations ... some sets (Donruss baseball for example) have 4 variations for almost every card. So you may add 1 to your collection, but depending on how you add it 4 may show up in your collection. On the top of the checklist page there is a drop down menu where you can select "Master set", here you can add the exact variation you have. Also from the same drop down menu box you can choose only to add cards for a specific variation.
I myself have not updated my 1989 Donruss (2 sets + shoe box full of doubles) because I know it's going to be a chore and will, more than likely, end up needing to wear glasses afterwards.
"They've done studies, you know. Sixty percent of the time it works every time." - Brian Fantana from the movie Anchorman