Mixed file formats in timeline not always playing nice.

Im using the latest version of premiere pro cc, and one of the great things about PP CC is that you can drop any file format in the timeline without trancoding it right? BUT! sometimes it doesn't play well when you add effects or titles, or adjustment layers. Lets say I have a 1080 DSLR timeline and I have a mix of H.264,ProRes and MP4 footage. When the footage is in the timeline with no effects, the playback is fine, but when I add a transition, a title or a adjustment layer over the footage, when it plays over that section, the footage sometimes stutters, or plays choppy. The footage will pause for a few frames an then continues, BUT only does this when effects are applied. Its behaves as if there is not enough frames to accommodate the transition or effect, which is not the case. But if I delete the clip and drop it into the timeline again in the same spot or I adjust the length of the transition the clip will play with no issues. Why is this happening? And yes ALL footage is rendered and I have powerful enough system to handle the work. Such simple effects should not affect timeline playback.

Hey Jim, with all do respect the symtoms may suggest that, as you stated but I know I have a powerful enough system. Im running a 8 core mac pro, 22gig ram,SSD drives and Radeon 5770 card. I have edited RED footage and Canon C500 footage with dynamic linked After effects on my system with no issues. So im certian its not my system.

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-I already read entirely those threads, but nothing about stereoscopic 3D AVCHD movies through USB port, on Panasonic TVPlasma3D.
(Also, Sony said me that is not possible to play 3D videos on your 3DTV through USB port).
I tried to made a H.264 videoclip, with .MP4 extension, at 960x1080p side-by-side layout, but nothing was displayed, and black screen.
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