How to get puff pastry to cook right through
A few points to consider...


Try docking the pastry.


  Docking means to pierce lightly with a fork, or a docker (looks like a spiked paint roller), to make small holes in dough that will let steam escape during baking. This helps the dough to remain flat and even.


ref: http://powerhungry.com/2009/02/puff-pastry-docking/
In general, to cook food more evenly, one should cook longer at a lower temperature. The problem is that the dough on the bottom of your crust is not reaching a high enough temperature by the time the top of your crust is done cooking.
Puff Pastry is notoriously finicky. Be sure to handle the dough according to puff pastry best practices to ensure the layers do not collapse and stick together.


Pepperidge Farm has a tutorial website (http://www.puffpastry.com/videos-and-tips#howto-demos) to help people with puff pastry issues, but it doesn't appear to cover much detail.


You must be very gentle when rolling out the pastry because it is
multiple layers of dough with fat between each.
Do not mangle the dough, cut clean lines and try not to apply pressure except where the knife is cutting
Do not let the dough get warm before you are ready to cook. The fat melts and the layers will stick and not puff properly.