Encore chapter markers off / different when playing DVD and when watching in Preview mode

I'm using CS6 and Encore version 6.0.0
I have a 120 min project with about 17 chapter markers. The markers were set to a older version of the project and then I extended the project by about 5 min and did a Replace Asset in the timeline. I adjusted the markers in the timeline. When I view the project in the Preview mode the chapters markers start at the right place but then I burn to DVD and they are off by about a minute.
I've tried deleting the cache and buring again but it's still off.
I think doing the Replace Asset messed things up but when it plays fine in Preview but not on the DVD something is really wrong.
Thanks

Update: I removed everything from the timeline and started over and entered the chapter markers. They are still off and now it's worse.
I have 21 chapters. 6-10 are off the rest are ok. I am burning to a dual layer DVD but I don't think that would be the reason.
Lastly, the DVD player skips over the final chapter it goes from 20 to the begining of the movie skipping Chapter 21.
What the heck?!

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