Produced DVD Exhibits Missing Music or Button Action, Even Though Check Project Tool and Play OK

Well, I have been successfully and faultlessly using Encore CS3 for several months, when all of a sudden my latest production suffers from the errors noted in the title; both Check Project Tool and "Play from Here" have always, in these problem cases, been OK. Just the discs weren't.
By the way, I am running this on a BOXX with dual Xeon 3.0, 4 gig ram, nVidia Quadro FX 1500, application on 10krpm 150 gig hd, and data on a slower 750 gig RAID 0, with everything cleaned and defragged, etc., etc. As yet, my problem is only with Encore, and not with more recently run Premiere (with Aspect HD), After Effects, Photoshop, and Ultra - nary, ever a problem with these! Also, never any problems with any DVDs, all burned 8X on a Sony writer, using DVD-R Verbatim discs. In the subject instances I assembled a disc format in Encore following my own self written 10 page procedure manual, step by step checklist, with ALL steps documented. So, I may be wrong, but I'm always consistant. And Check Project Tool, and preplay in Encore no errors, and worked perfectly, as usual.
But first burned disc played no audio on the main menu, while chapter menu music (from same source file as usual), was fine. And motion pictures in both main and chapter menus worked fine. Soooooo, complete recheck of project showed everything fine, and same Adobe checks worked fine, and another burned disc, same fault.
So, uninstalled Encore CS3, including preferences, etc., and re-installed. And brought in everything again, and reconstructed the structure from scratch again, and everything tested fine. Then I burned a test disc, 1 pass low rate Adobe Media Encoder converting from 1080i .avi to 480i, and the disc played perfectly! BUT THEN........ I reincoded at vbr 2pass, high quality, and burned twenty discs at 480p. And everything plays fine, EXCEPT, on all four of my test DVD players, the "timeline" plays fine, video and audio, the main menu pictures and music and "Play Movie" and "Chapter Selections" buttons all work, but although the Chapter Sub-menu pictures and music are as intended, the "Chapter 1" button is highlighted, as intended, but you can't move from there to the other chapters button or the button to return to the main menu.
And again, these all worked fine when the Check Project Tool was utilized just prior to setting up the DVD files and burning - and no, I touched NOTHING else in the meantime.
So, that's my story, and I'm sticking to it.
And I would certainly appreciate insights from anyone about what the matter might be (besides Microsoft), so long as the insights are thought provoking, whether they are valid or not.
But seriously, this has me stumped. And I really will NEVER, ever burn and print (full color!) 20 discs again without fully testing the first one burned and then never change anything in Encore.

Harm - thanks for the suggestion!
Given what I now know about transcoding and interlace effects, 480i insead of 480p is totally unacceptable to me, for excellent reasons explained in a moment. If Encore only works correctly with 480i (anyone have any thoughts as to why that might be true?) then its time for me to drop Encore and move on to another DVD assembler. I'd not care to do this, as I finally have all study of Encore and my related procedures manual put together, and I would certainly miss some of the fine and relatively easy features of Encore, to say nothing of the use of PixelPops panels in Encore. One other point. I badly mis-spoke myself in the original post, and I apologize for that. I should have said that Adobe Media Encoder was being used within Encore to encode from 1080p, not 1080i. More about all that in a moment.
So, I now have a further question, if I cannot get a work around for this. Anyone have any thoughts on an alternate DVD assembler with a decent transcoder, for $1,000 or less? No matter what, I intend to continue to use other Adobe products.
Now, as to why 480p! And I may just run an informational post about this sometime. Several weeks ago I had finally decided that what I had been putting together as 480i was just totally unacceptable because of the deinterlacing artifacts shown when run through the standard DVD player and typical LCD screen. The noise, particularly the misquito noise, the twitter, etc. was just too much. So I set aside three days, and all I did was run tests of various sequences of transcoding 1080i to 480 whatever. And of all the permutations and combinations, the clearly superior result was the following. As our friends at Cineform have so rightly commented, going from 1080 to 480 gives us all kinds of headroom to work with. So my current procedure is to first take the Cineform "visually perfect" 1080i .avi files and using the Cineform transcoder, convert them to 1080p.avi. Then, as noted above, I use the Adobe Media Encoder to go from 1080p to 480p. Now that picture, I am really happy with! And by the way, what is produced by using the Adobe Media Encoder to transcode directly from 1080i to 480p is truly grotesque - the horizontal distortion is so horrible it has to be seen to be believed! Other variations produced from good to marginal results. The closest acceptable was using Cineform to go from 1080i to 1080p and then to 480i, and then using AME to go from 480i to 480p DVD.
By the way, the final, best otherwise encoded 480i result showed up only marginally better than what I am doing now, when shown on a 109 inch screen using that great chip in the latest Toshiba HD-DVD player for the deinterlacing function. But when the same disc was played on your typical consumer DVD player and flat panel screen, the result was marginal. I have read many places that we are better off letting the consumer players or screens conduct the deinterlacing of our 480i productions, instead of producing 480p discs ourselves. Given the transcoders I currently have to work with, I would say that is just nonsense. If all the consumers had players with great deinterlacers that would be true. But it isn't true!

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