Whenever I cast Prayer in Pool of Radiance, it only affects the casting cleric. (I believe someone else had mentioned this for some of the Krynn games but there the problem was when it was cast in combat, not out of combat. I also think someone on the Steam boards mentioned seeing this in GBC). Does anyone know anything about this?

That's just how the Gold Box series displays the effect. Prayer in 1st Edition AD&D always affects all allies and all enemies regardless of range or line of sight.

The real strangeness is when it affects the entire party in exploration mode. You should be able to drop your Cleric from the party, and then the Prayer effect goes away with him. It doesn't until some of the later games.