You receive coins to address x. You put address x on paperwallet.
Then you spend a part of the bitcoins on address x. The "change" is sent back not to address x but to a NEW one. Why? For anonimity. Nothing of course stop the client from sending the change to the address x, but this is not how the bitcoin-qt client work. It does not even offer the option to send it back to x address... and almost no one know about this thing.
Now, if you later lose the wallet on bitcoin-qt and you use the paperwallet, well, btc no more are on that address... they are on a new one. Surprise
![Cheesy](https://bitcointalk.org/Smileys/default/cheesy.gif)
And that new one of course is not on the paperwallet.
As you notice by reading that thread there are some services who send the btc back to address x