Thanks for your response, Tom.
If you were to install Notability on your iPad mini and it still exhibit the shrinking behaviour we could (tentatively) say that the non-retina screen iPads don't have this problem in either iOS 9.2.1 or 8.4.1, whether or not they have Notability. That would be helpful to establish. (I could also upgrade our iPad 2 to 9.2.1 to check this, but I'm slightly reluctant to do so as it is next to impossible to downgrade these things and it is sometimes helpful for our testing for us to have a machine with an older OS.)
Our users who notified us of this problem (and who use a class set of iPad Air's apparently--so retina screens) said they thought this problem first exhibited itself 'about three months ago'. Although they haven't told me whether or not it was after an OS upgrade (or a Notability upgrade?) that the shrinking began, according to Wikipedia iOS 9.0 was introduced in September last year (5 months ago) and iOS 9.1 in October (4 months ago) and iOS 9.2 in December (2 months ago), finally 9.2.1 was last month. It seems quite plausible then that this might be related to something introduced in iOS 9.1 or 9.2. Notability appears to get upgrades about once a month. Would any of the above fit with you experience, Tom? Do you remember when you upgraded, or might you have noticed the shrinking behaviour beginning soon after?
It does seem that they were using our iBooks & widgets alongside Notability without problem before then, so I guess something new caused it. There were a couple of changes to iBooks mentioned in the iOS 9.2 upgrade in December (though at first glance it isn't obvious that they should have had this effect). Currently they are the only people who have complained about this to us, but it is possible that we simply haven't heard yet, or perhaps many of our users (mostly classroom sets of iPads in schools) are not regularly switching between our app and other apps in this way.
We have relatively few apps on our two iPads as they are mostly used to test our iBooks books while we're authoring them. I'm pretty certain we don't have any of the apps you mention above.
It does look as though the problem may turn out be something to do with the retina screen and a recent-ish software upgrade...?