Got burned on two versions of the same bug today CS6....
I had entered a .jpeg still instead of video clip into video of menu... That resulted in automatic playing of a selection on the menu when I ran the software player... no error messages, just didn't work in player.
I finally compared an older project where menu video was replaced, and saw an H264 video clip instead of .JPEG.
That fixed it!
Also, a second 'feature'... I had first saved an MPEG video, which I believe was MPEG codec from MXO2 capture card. That showed video for a flash, then went black. Changed to H264 and problem went way... Again, no error messages, just didn't work correctly...
When in doubt, recall session that did work, and see what's different!
Encode video clips for Encore using MPEG-2 DVD format, which is an .m2v file. Putting anything else into Encore is looking for problems - it will transcode anything else anyway, so why not give it what it wants?
The symptom (automatically playing Button #1) when a jpeg was placed on video path, was so strange... It displayed perfectly, so who would know it was that? I thought after I'd found the cause, that it might be nice to post about it to prevent someone else from falling into the trap I just had... I just assumed that the MPEG thing from 2nd occurrence was the MXO2 MPEG Codec issue, as screen went black. There again, posting it gives info to other's about a bug we'll have to live with!