Using CloneDVD 2.6.2.3 and AnyDVD 4.5.5.1.

This is the first time I've used this particular combination to transcode a DVD and found that when testing the output [to DVD files] that PowerDVD kept returning me to the beginning of the movie when I used the chapter search function [right click on the 'next chapter' button and select a chapter to jump to], I was playing the DVD files direct from the Hard Disk. It has done this consistently across 3 seperate DVDs so far. Skipping the chapters one at a time is fine, but searching forward or backward more than 1 chapter sends the movie back to the beginning.

Cloning the main movie only and preserving the menus. AnyDVD is set to jump to the title menu and remove everything except PC-Friendly.

Any ideas?

Orinico,
How about trying to use the "Jump directly to Main Movie" in AnyDVD.
If that does not work, uncheck the "remove annoying adverts and trailers."
I personally always keep all the boxes in "Feature Removal" checked, including PC-Friendly.

The below quote from James at Slysoft may be related:
“Changing the DVD structure automatically is tricky and will not work with every DVD. This is documented in AnyDVD's online help (right mouse button).
Jumping to the main movie does not work, if the "main movie" can not be identified (TV episodes, widescreen & fullscreen on one disc).
Jumping to the title menu does not work, if the DVD does not have a title menu.
Some DVDs have special checks, which prevent a direct jump (they check, if certain variables are set in the pre-commands of the program chain, and will do an "own jump" if these variables are not set).
We are trying to improve this function, but it will probably never work with every DVD.
__________________
James”

You can read the whole post here:
http://club.cdfreaks.com/showthread.php?t=123589

Good thinking itzbinnice, but sadly the removal of annoying adverts and trailers is not the answer. I've ripped one of the problematic movies again without that feature ticked and the output still returns to the beginning of the movie.

Burning both rips to a -RW and testing them in a 'real' DVD player showed no problem with chapter searching.

In fact exiting AnyDVD still causes the same behaviour in PowerDVD when playing the original disk. I'm amazed it played at all as the drive it was playing in is RPC1 so I would have expected PowerDVD to complain about the region mis-match. CloneDVD was not able to rip the disk without AnyDVD running [as you would expect], making me wonder what is going on with PowerDVD........

Sorry, don't know what else to suggest, maybe somebody else can jump in and offer some advice. This could very well be movie specific, as James mentions.
You can always try uninstalling then reinstalling PowerDVD, perhaps something became corrupt.