thanks for the information and i might be able to help you. but before i can, we must pray.
start of prayer:
keynote v6 and iba 2.3 didn't mix well. there were tons of problems. i tried it in nov 2014 and i could not drag and drop a keynote file that contained audio or movie into the keynote widget. i went to the support but they brushed me off and told me to recreate everything and that it must be my fault. instead, i continued to use v5. come july 2015, i bit the bullet and upgraded everything because i didn't think it was a good idea to send my book to the store with old software. i thought i was near finished but i was not as evidence that now i am near finish and been working long hours since end of july. the month of jul was a complete washout. think your two weeks just wasted and double it. i got nothing done as i spent all my time working with apple to report bugs.
bug 1: same bug i discovered in november. i stumbled upon the workaround. i happened to mention this to a level 2 guy while working on another problem and he was all over me to tell him the workaround. he was a decent guy (they probably most are) and we was grateful. the workaround is that the file has to be opened at the time. i then sent apple support a notarized letter (well, maybe it was just an ordinary email), complaining about the brush off in november and how they did not make the necessary effort to help me on something that they could have easily solved. they had monkey off the back syndrome. please note: their support is usually better than this, especially when it is a user error. it was not a user error in this case.
bug 2: audio and movies would only play once and not loop if that was chosen. a real bummer for me. same as you, it worked in keynote but not once it was dropped into the widget.apple gave me a workaround.
bug 3: i could not use preview button to go to the iPad. with the help of someone on this community (tom) i used another means to get it there: preview to mac and then sync to iPad.
bug 4: because of bug 2, gifs stopped working past the first cycle. had to convert them to movies. pain in the you know what.
bug 5: i've had problems even before v6 with the same audio file being used on different slides in keynote, once dropped into a widget. apple used to change the suffixes at some point. after july i took a different path where i converted to a different suffix when i needed this.
bug 6: nothing to do with apple, but the workaround apple give me caused a problem with math type. i called the math type people. they sounded real responsive but never heard back from them. this caused me to do some compromising. after i finish my book, i will take this up with them again if it is still a problem.
i am totally afraid of going to any new releases as i cannot afford to delay what i thought would be done by september 2014 and now perhaps dec 2015. apples reliability, availability and serviceability is not what it should be for us and going forward have decided to purchase a test system to test out new releases before i move new releases to my production machine. it is so bad that i am even afraid of my shadow now.
this has all been documented by me before on this site, but i thought i would do it again to save you the time to find it. i do not know what if any of these problems have now been fixed but do know that your problem has been introduced at some point. i heavily used this linking facility in a book i published in 2013 but only branch to a slide and then back to the branch from point. i did away with this navigation in the book i have been working on since then.
end of prayer
rather than wait for apple to fix this, which could be awhile, it might just work with the workaround they gave me. once you have your keynote done, instead of drag and drop, do this:
1. in keynote, use file menu export to 09. this creates a v5 compatible keynote. if this bug was not present at this release of keynote/iba interaction, then drag and drop this exported keynote into the widget. either it works or does not work. if it does work, the problem is likely in the interfacing of the new keynote to iba. if it does not work, the problem probably already existed in v5 (keynote 09). this of course only if the keynote does not use any features new to v6 that was not in v5 or you can't replace the new features. and only if the latest keynote still has this export to keynote 09 file menu item. i don't know as i'm scared.
let me know if this works if you can as i am interested. i do hope it does.
i do have a question as to why you are using links to traverse your slides in a serial manner whether back or forth in iba or for that matter in keynote. why not just use the built in swipe command of the iPad. for me i think if both were available, i would swept where i wanted to rather than have to move my hand to a button. if someone was reading you book on the mac instead of an iPad, the mac implementation of ibooks already has these buttons so you will have then twice.
