Some Blu Rays are mastered better than others. The cartoons tend to have a digital source, whereas Flying Daggers and POTC are most likely film based - meaning encoding errors are prone to pop up, especially if the movie is a "legacy" film (mastered into digital without the forethought of a later high def version). I have only heard good things about the POTC discs, though.
Make sure that your Blu Ray player is set to output in either 720p, 1080i, or 1080p - whatever your TV's max resolution is and make sure that it isn't downconverting the movie into 480p or anything.
Also make sure (I'm sure this is the case) that you have it hooked up with at least component (HDMI even better) cables. (This last bit is pretty remedial, and I apologize for that, but you never know).
The bottom line is that some discs are just mastered better than others. Why they spent so much time on the dreck that is Con Air and (apparently) so little time on the visual jewel that is Flying Daggers, is a mystery to me.
