Having the same problem. Using MXF video files from the Sony F5. Was never a problem until the past few months and seems to be getting worse as time goes on. I've tried Premiere Pro CC (2014), and using the previous Premiere Pro CC (hoping it may work like it used to) and no luck.
Any ideas, solutions, help at all would be greatly appreciated. It's to the point where some projects I can't even watch all the way through. I just have to guess that it is right and hope the video exports so I can view it that way. I have to save after ever step, before renders and pretty much any time I click the mouse. It's making Premiere absolutely useless. Edits that should take a few hours take days now.
After Effects has no troubles at all using the exact same footage and seems to be operating flawlessly. .
It is a pity that no one from adobe is answering this post. Anyway, having made testings found the following
1) It happens on the mac ( not the PC )
2) I found the following sequence settings to degrade the problem to 20% ( I mean the codec - Apple pro res 422
3) To eliminate the problem I import the files and while logging, and starting a first cut, i convert them in backround ( using Mpeg Streamclip - personal choice ) at Apple pro res 422 (any flavor) and when this is done i simply reconnect them to the Pro res ( using the above settings ) and problem gone...
But all the above is a roundtrip not a solution. If anyone from Adobe is out there...:)