cream pies

Unfortunately you can't fix this now. Did your filling contain eggs? If so, I'm pretty sure that the reason they're still runny is that you didn't cook it long enough. Eggs contain an enzyme, alpha-amylase, that if not totally inactivated, will destroy the starch network of your custard. Even it looks nice and thick when you pour it into the shell, any enzyme not inactivated will catalyze and re-thin the filling. In order to inactivate all the enzymes, the entire mixture needs to come to above 180 degrees (and this is the important part) all the way through. By the way, this has happened to me also! In fact, I gave up on cream pies completely, convinced it would never get them right, until I saw an episode of Good Eats where Shirley Corriher explained this reaction.

No don't think freezing will make a difference if the chilling didn't.

Have you tried chilling them in the fridge?