Sporadic problems rendering HD video files...need a set of do's and don'ts

[acfalk]

Issue: Sporadic problems rendering HD video files when producing a Blu-ray DVD using Photodex ProShow Producer or Roxio's Creator Pro.
I make Blu-ray DVDs from my own Canon HD Vixia HF S10, and from HD downloads from YouTube that usually are mp4 files. I use both the Photodex and Roxio softwares above in producing projects usually less than an hour long. Frequently there will be a video file or two that will cause a problem, like a freeze in the rendering, or refusing to accept an edit.
Is there anyone out there that has developed a good list of do's and don'ts regarding working with file types? Are there some file types with certain profiles (like a particular video codec, a particular frame rate, etc.) that really have to be converted to something else to work with? And are there some file types that we mortals just should not try to edit or truncate at the start or the end regarding stability?
This moderately experienced amateur would like to see a set of do's and don'ts for working with HD files.
Thanks very much
Chuck Falk
Aiken, SC