That's simplifying the issue too much.
We've had these problems in all post production-related tasks. Simple playback is usually not the issue, but exotic formats have always been supported either in a less usable fashion or not at all.
VLC probably uses the most recent FFMPEG libraries, which are likely to be more efficient and compatible. Plus, it's a video player that has matured over the last ten years or so. It is built to play everything.
I don't think Reaper is. And poorly chosen codec/container formats will play less well in any DAW. I've tried to write down recommendations that seemingly work well, in terms of which FFMPEG build to use, which codec/container combos work well for certain tasks.
My recommendation for a conversion program still stands however, and that is MPEG Streamclip.
VLC is rather difficult to setup and operate, and I'm not even sure the results are very compatible with anything, i.e. I know nothing about that.
MPEG Streamclip can generate legal Quicktimes and a huge bunch of other container/codec combos. You'll be much better off using that. It's free and available for both Windows and OSX.
Btw, I've used HD MP4 files as well, but there seem to be a range of different kinds, but it's been a while since I ran in to a nasty one. I get mine from either Vegas, After Effects or the Adobe Media Encoder. The stuff from Youtube is great too (MP4 downloads). If the seeking is too slow for my work, I convert them with MPEG Streamclip in to a Quicktime/PhotoJPEG or Quicktime/H264(with keyframe distance 0).
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