It's been a very long time since I've used InDesign... I was a PageMaker "fan" — did not care much for the Adobe copycat. Adobe has this "thing" — you can create files that are optimized for other Adobe products (this is the default behavior), or you can make a choice for "Maximum Compatibility". Rather vague wording, but I'm fairly sure you need to make sure that option is selected when saving as a PDF (IF that is even an available option in InDesign — but it sure is in Photoshop, at least the last version I used [CS6]). If that option is not available, try opening the PDF in Preview and Export a copy to use in Motion (as this should make it more Mac compatible). Make sure what you see in Preview is what you need in Motion!
I'm also assuming that when you say you used Media > Properties > Page Number you really meant [pdf selected in *Layers List*] > Properties > Media > Page Number (because I don't think you are able to select a page number from within the Media tab.)
About your main question: I'm fairly sure that the internal file "storage" format for PDFs in Adobe products is proprietary and I will venture that guess that they are not linear (or, exactly as you visually lay out the document) and always subject to change. That is Adobe's "right". Historically, for many (*many*) years, PDFs were the sole domain of Adobe's. The first non-Adobe apps that could (merely) open PDFs were all hacks and not even remotely guaranteed to work correctly. So, it is a very difficult file format to parse. Adobe finally loosened its iron-clad hold on PDFs for better cross application (and web) compatibility (hence the appearance of the Maximize Compatibility option [check preferences]), but I wouldn't trust any PDF created in an Adobe app *optimized* for Adobe products to be useful anywhere else.
I am 99.99% sure the problem is NOT Motion.
