This is not an easy question to answer as there can be several reasons causing this type of problem, in my experience this can be caused by the following conditions, though I have found that my PC seems to cope better on copied movies than my stand alone player.
My first panasonic DVD player would play 9 out of 10 movies fine then it would play the 10th with about a 2 second gap OOS this was a problem I experienced with both copied and original media.
Problems with stand alone reading from +/-r media
Bad media or poor writing of media.
Bad capture / conversion or compression of original movie
There are more reasons than these but these are the main ones I have encountered but a trick I have learnt is that if you eject the DVD and then re-insert it it can sometimes improve or completely disappear.
As to are these caused by authoring programs it depends on which one your using and what your trying to do with it.