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
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