Can you please add the following info:
System specs. in detail
The full specs. on the MP4 files, both those that do work and those that do not - how are they different?
Your Sequence Preset
This ARTICLE will give you some tips on the types of info, that would be so very useful to us.
Also, can you tell us which H.264 CODEC you have installed?
Good luck, and we'll be looking for that very important info,
Premiere uses a lot more of your computer resources ( memory and cpu and video card ) than media player, because it's a fairly high end video editing program. What version are you using ? What kind of computer do you have, cpu , ram, video card, etc. ?
Please give more info and some people here can try to help you.
Yes. Too many people are lulled into a false sense of security, because a file will play in a media player, but an NLE will have issues with it. Playing a file is a simple task. Editing that same file is anything but a simple task. Also, many CODEC's will only work for playback, and most NLE's (like PrPro) cannot use them to edit. Whether the NLE can, will depend on the NLE. PrPro will not successfully edit DivX, but CyberLink's PowerDirector can often do so. Just a difference between the programs.
Again, playback of a media file is no guarantee that that same file can be edited - totally different operations.