Actually the correct quote is:
Penalties do not have a type and most penalties stack with one another.
The "with one another" meaning two separate penalties (i.e. different sources).

To my knowledge a penalty is nothing more than a negative bonus (a malus if you will) and the rules state that the same principles apply (can't find which section, perhaps under magic).

Besides, it would be a nightmare keeping track of the penalties if those from the same source stacked. You can sneak attack like 5 times in a round and each would have a different duration. I doubt Paizo is training us to be accountants.