I'm sure there will be some animations that won't work exactly right for fixed layout epubs. If you can replicate this, you should report it as a bug (and link to a sample file):
In the meantime, is it possible to move your animation to the pasteboard, and manipulate its flight path to end up in the correct location? That might work.
Thanks for reaching us out on this forum. Could you please send us your test document so that we can investigate this further? You can either send me the packaged InDesign content directly or upload it to dropbox. My email id is: email@example.com
A question: does your problem appear only on odd pages?
I have the same issue on ipad pro 12.9 (ios10).
The textbox is visible, disappears, and then it animates :/
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I had a similar problem with the first fly-ins and fade-ins appearing, disappearing, and appearing. They were graphics. The fix was to uncheck the hide until animated box (checking it had been a desperate attempt to get the animations to work but never should have been needed) and add a delay of .25 secs to the first animated item, which isn't noticeable.
Has anyone found a solution to this yet? I'm still having the animation problems when exporting to iPads!
If it works everywhere else, my assumption would be that it’s iBooks on iOS issue.
Have you checked the Apple forums?
I have just checked the Apple forums and think the base issue lies with iBooks not being particularly well suited to opening ePubs. I will research further and try using other ePub readers and report back!
Okay, so after playing around with a few apps it seems that the best for displaying working animations on iPads is Adobe Digital Editions. However, its not exactly smooth when it comes to swiping pages and even blank pages have a slight loading time.
I'm a bit disappointed in all honesty as I feel iBooks is still the best reader for viewing documents smoothly. It looks like the only 'fix' is to remove animations all together for iPad fixed layout ePubs.