Hey to you TimC,
My guess is that a guy with as high a post count as yours already knows alot about backing up but is just recently transitioning to DL burning.
"Pressed" original DVDs have the highest level of read compatibility with DVD players and even they have about a half second layer-transition hesitation. You may not have noticed it because when they master the DVD they try to choose a "still" part of a scene (like when the camera is focused on a distant still landscape or during a fade-out between scenes) in which to place the layer break point. This hesitation happens because the player's laser beam mechanism must re-focus downwards, to read layer#2 which is a fraction of a milimeter below layer#1, which results in a slightly perceptable hesitation.
It is not unusual for a burned backup disk to hesitate a bit more during the layer transition because burned disks are less readable than pressed disks. My verdict: Normal behavior, nothing to worry about.
... Created an ISO image with PGCEDIT to reposition the layer break. ...
This part of your post is probably most responsible for a longer than normal hesitation. You are using a "software created" i.e. "artificial" layer break point which the player takes longer to read & react to than if you had simply copied using the "original" DVD's break point. I think, at the outside edge of layer#1, there is a "layer break coding" on the disk that sends a command to your player to refocus the laser beam to layer#2. I submit that any ISO file created with other than a 1:1 mirror of the original is not a true ISO file. Fine for watching the movie on a computer, from the HDD. But depending on the backup software used, can create layer break freezups or slower than normal transitions (the later being not a big problem at all).
My opinion is that the creation of ISO files should be used to create a mirror "image" ... suggest you don't change the break point or remove any features or audio/sub tracks. Removing data, by definition, causes or requires an alteration in the original layer break (software automatic or manual like you did). The original mastered DVD has already figured out the optimal postitioning of data on layers #1 & #2. Why muck around with it? Just duplicate it 1:1 with DVD-D/ImgBurn in ISO mode or Elby/Slysoft CloneCD which is ISO only. If you are changing things around on your backup, you are transcoding (so to speak), not creating a mirror ISO file.
In summary, I don't think your problem is a problem unless you start getting freeze-ups at the layer transition point of your backups.
BTW, suggest using Verbatim +R DL media (bitset/booktyped to DVD-ROM format) and burning at half the rated speed of the media.